
#############################################################################
# LASTZ chicken/galGal6 vs Rifleman/acaChl1 - (DONE - 2018-10-16 - script/hiram)
    mkdir /hive/data/genomes/galGal6/bed/lastzAcaChl1.2018-10-16
    cd /hive/data/genomes/galGal6/bed/lastzAcaChl1.2018-10-16

   printf "# chicken vs Rifleman
# galGal6 vs acaChl1
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.00/bin/lastz
BLASTZ_H=2000
BLASTZ_Y=3400
BLASTZ_L=4000
BLASTZ_K=2200
BLASTZ_M=254
BLASTZ_Q=/cluster/data/blastz/HoxD55.q

# TARGET: galGal6 - chicken - Gallus gallus
SEQ1_DIR=/hive/data/genomes/galGal6/galGal6.2bit
SEQ1_LEN=/hive/data/genomes/galGal6/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
SEQ1_LIMIT=40

# QUERY: acaChl1 - Rifleman - Acanthisitta chloris
SEQ2_DIR=/hive/data/genomes/acaChl1/acaChl1.2bit
SEQ2_LEN=/hive/data/genomes/acaChl1/chrom.sizes
SEQ2_CHUNK=1000000
SEQ2_LIMIT=2000
SEQ2_LAP=0

BASE=/hive/data/genomes/galGal6/bed/lastzAcaChl1.2018-10-16
TMPDIR=/dev/shm
" > DEF

    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
      -workhorse=hgwdev -bigClusterHub=ku \
        -dbHost=hgwdev -smallClusterHub=ku \
          -fileServer=hgwdev -syntenicNet) > do.log 2>&1
    # real	641m40.810s

    cat fb.galGal6.chainAcaChl1Link.txt
    # 839072309 bases of 1055588482 (79.489%) in intersection

    cat fb.galGal6.chainSynAcaChl1Link.txt
    # 680540676 bases of 1055588482 (64.470%) in intersection

    time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \
	galGal6 AcaChl1) > rbest.log 2>&1 &
    # real	470m51.711s

    cat fb.galGal6.chainRBest.AcaChl1.txt
    # 740532507 bases of 1055588482 (70.154%) in intersection

#############################################################################
# LASTZ chicken/galGal6 vs Japanese eel/angJap1 - (DONE - 2018-10-16 - script/hiram)
    mkdir /hive/data/genomes/galGal6/bed/lastzAngJap1.2018-10-16
    cd /hive/data/genomes/galGal6/bed/lastzAngJap1.2018-10-16

   printf "# chicken vs Japanese eel
# galGal6 vs angJap1
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.00/bin/lastz
BLASTZ_H=2000
BLASTZ_Y=3400
BLASTZ_L=4000
BLASTZ_K=2200
BLASTZ_M=254
BLASTZ_Q=/cluster/data/blastz/HoxD55.q

# TARGET: galGal6 - chicken - Gallus gallus
SEQ1_DIR=/hive/data/genomes/galGal6/galGal6.2bit
SEQ1_LEN=/hive/data/genomes/galGal6/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
SEQ1_LIMIT=40

# QUERY: angJap1 - Japanese eel - Anguilla japonica
SEQ2_DIR=/hive/data/genomes/angJap1/angJap1.2bit
SEQ2_LEN=/hive/data/genomes/angJap1/chrom.sizes
SEQ2_CHUNK=1000000
SEQ2_LIMIT=2000
SEQ2_LAP=0

BASE=/hive/data/genomes/galGal6/bed/lastzAngJap1.2018-10-16
TMPDIR=/dev/shm
" > DEF

    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
      -workhorse=hgwdev -bigClusterHub=ku \
        -dbHost=hgwdev -smallClusterHub=ku \
          -fileServer=hgwdev -syntenicNet) > do.log 2>&1
    # real	157m11.534s

    cat fb.galGal6.chainAngJap1Link.txt
    # 57085539 bases of 1055588482 (5.408%) in intersection

    cat fb.galGal6.chainSynAngJap1Link.txt
    # 8699962 bases of 1055588482 (0.824%) in intersection

    time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \
	galGal6 AngJap1) > rbest.log 2>&1 &
    # real	85m42.406s

    cat fb.galGal6.chainRBest.AngJap1.txt
    # 43283102 bases of 1055588482 (4.100%) in intersection

#############################################################################
# LASTZ chicken/galGal6 vs Stickleback/gasAcu1 - (DONE - 2018-10-16 - script/hiram)
    mkdir /hive/data/genomes/galGal6/bed/lastzGasAcu1.2018-10-16
    cd /hive/data/genomes/galGal6/bed/lastzGasAcu1.2018-10-16

   printf "# chicken vs Stickleback
# galGal6 vs gasAcu1
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.00/bin/lastz
BLASTZ_H=2000
BLASTZ_Y=3400
BLASTZ_L=4000
BLASTZ_K=2200
BLASTZ_M=254
BLASTZ_Q=/cluster/data/blastz/HoxD55.q

# TARGET: galGal6 - chicken - Gallus gallus
SEQ1_DIR=/hive/data/genomes/galGal6/galGal6.2bit
SEQ1_LEN=/hive/data/genomes/galGal6/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
SEQ1_LIMIT=40

# QUERY: gasAcu1 - Stickleback - Gasterosteus aculeatus
SEQ2_DIR=/hive/data/genomes/gasAcu1/gasAcu1.2bit
SEQ2_LEN=/hive/data/genomes/gasAcu1/chrom.sizes
SEQ2_CHUNK=1000000
SEQ2_LIMIT=2000
SEQ2_LAP=0

BASE=/hive/data/genomes/galGal6/bed/lastzGasAcu1.2018-10-16
TMPDIR=/dev/shm
" > DEF

    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
      -workhorse=hgwdev -bigClusterHub=ku \
        -dbHost=hgwdev -smallClusterHub=ku \
          -fileServer=hgwdev -syntenicNet) > do.log 2>&1
    # real	130m29.417s

    cat fb.galGal6.chainGasAcu1Link.txt
    # 48797842 bases of 1055588482 (4.623%) in intersection

    cat fb.galGal6.chainSynGasAcu1Link.txt
    # 13482396 bases of 1055588482 (1.277%) in intersection

    time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \
	galGal6 GasAcu1) > rbest.log 2>&1 &
    # real	79m45.934s

    cat fb.galGal6.chainRBest.GasAcu1.txt
    # 38052220 bases of 1055588482 (3.605%) in intersection

#############################################################################
# LASTZ chicken/galGal6 vs Turkey/melGal5 - (DONE - 2018-10-16 - script/hiram)
    mkdir /hive/data/genomes/galGal6/bed/lastzMelGal5.2018-10-16
    cd /hive/data/genomes/galGal6/bed/lastzMelGal5.2018-10-16

   printf "# chicken vs Turkey
# galGal6 vs melGal5
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.00/bin/lastz
BLASTZ_H=2000
BLASTZ_Y=3400
BLASTZ_L=4000
BLASTZ_K=2200
BLASTZ_M=254
BLASTZ_Q=/cluster/data/blastz/HoxD55.q

# TARGET: galGal6 - chicken - Gallus gallus
SEQ1_DIR=/hive/data/genomes/galGal6/galGal6.2bit
SEQ1_LEN=/hive/data/genomes/galGal6/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
SEQ1_LIMIT=40

# QUERY: melGal5 - Turkey - Meleagris gallopavo
SEQ2_DIR=/hive/data/genomes/melGal5/melGal5.2bit
SEQ2_LEN=/hive/data/genomes/melGal5/chrom.sizes
SEQ2_CHUNK=1000000
SEQ2_LIMIT=2000
SEQ2_LAP=0

BASE=/hive/data/genomes/galGal6/bed/lastzMelGal5.2018-10-16
TMPDIR=/dev/shm
" > DEF

    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
      -workhorse=hgwdev -bigClusterHub=ku \
        -dbHost=hgwdev -smallClusterHub=ku \
          -fileServer=hgwdev -syntenicNet) > do.log 2>&1
    # real	91m10.856s

    cat fb.galGal6.chainMelGal5Link.txt
    # 997476452 bases of 1055588482 (94.495%) in intersection

    cat fb.galGal6.chainSynMelGal5Link.txt
    # 715177000 bases of 1055588482 (67.751%) in intersection

    time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \
	galGal6 MelGal5) > rbest.log 2>&1 &
    # real	251m2.883s

    cat fb.galGal6.chainRBest.MelGal5.txt
    # 909544688 bases of 1055588482 (86.165%) in intersection

#############################################################################
# LASTZ chicken/galGal6 vs Lamprey/petMar3 - (DONE - 2018-10-16 - script/hiram)
    mkdir /hive/data/genomes/galGal6/bed/lastzPetMar3.2018-10-16
    cd /hive/data/genomes/galGal6/bed/lastzPetMar3.2018-10-16

   printf "# chicken vs Lamprey
# galGal6 vs petMar3
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.00/bin/lastz
BLASTZ_H=2000
BLASTZ_Y=3400
BLASTZ_L=4000
BLASTZ_K=2200
BLASTZ_M=254
BLASTZ_Q=/cluster/data/blastz/HoxD55.q

# TARGET: galGal6 - chicken - Gallus gallus
SEQ1_DIR=/hive/data/genomes/galGal6/galGal6.2bit
SEQ1_LEN=/hive/data/genomes/galGal6/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
SEQ1_LIMIT=40

# QUERY: petMar3 - Lamprey - Petromyzon marinus
SEQ2_DIR=/hive/data/genomes/petMar3/petMar3.2bit
SEQ2_LEN=/hive/data/genomes/petMar3/chrom.sizes
SEQ2_CHUNK=1000000
SEQ2_LIMIT=2000
SEQ2_LAP=0

BASE=/hive/data/genomes/galGal6/bed/lastzPetMar3.2018-10-16
TMPDIR=/dev/shm
" > DEF

    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
      -workhorse=hgwdev -bigClusterHub=ku \
        -dbHost=hgwdev -smallClusterHub=ku \
          -fileServer=hgwdev -syntenicNet) > do.log 2>&1
    # real	123m7.872s

    cat fb.galGal6.chainPetMar3Link.txt
    # 38618644 bases of 1055588482 (3.658%) in intersection

    cat fb.galGal6.chainSynPetMar3Link.txt
    # 1678799 bases of 1055588482 (0.159%) in intersection

    time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \
	galGal6 PetMar3) > rbest.log 2>&1 &
    # real	61m19.652s

    cat fb.galGal6.chainRBest.PetMar3.txt
    # 26040801 bases of 1055588482 (2.467%) in intersection

#############################################################################
# LASTZ chicken/galGal6 vs White-throated sparrow/zonAlb1 - (DONE - 2018-10-16 - script/hiram)
    mkdir /hive/data/genomes/galGal6/bed/lastzZonAlb1.2018-10-16
    cd /hive/data/genomes/galGal6/bed/lastzZonAlb1.2018-10-16

   printf "# chicken vs White-throated sparrow
# galGal6 vs zonAlb1
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.00/bin/lastz
BLASTZ_H=2000
BLASTZ_Y=3400
BLASTZ_L=4000
BLASTZ_K=2200
BLASTZ_M=254
BLASTZ_Q=/cluster/data/blastz/HoxD55.q

# TARGET: galGal6 - chicken - Gallus gallus
SEQ1_DIR=/hive/data/genomes/galGal6/galGal6.2bit
SEQ1_LEN=/hive/data/genomes/galGal6/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
SEQ1_LIMIT=40

# QUERY: zonAlb1 - White-throated sparrow - Zonotrichia albicollis
SEQ2_DIR=/hive/data/genomes/zonAlb1/zonAlb1.2bit
SEQ2_LEN=/hive/data/genomes/zonAlb1/chrom.sizes
SEQ2_CHUNK=1000000
SEQ2_LIMIT=2000
SEQ2_LAP=0

BASE=/hive/data/genomes/galGal6/bed/lastzZonAlb1.2018-10-16
TMPDIR=/dev/shm
" > DEF

    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
      -workhorse=hgwdev -bigClusterHub=ku \
        -dbHost=hgwdev -smallClusterHub=ku \
          -fileServer=hgwdev -syntenicNet) > do.log 2>&1
    # real	414m13.921s

    cat fb.galGal6.chainZonAlb1Link.txt
    # 830165711 bases of 1055588482 (78.645%) in intersection

    cat fb.galGal6.chainSynZonAlb1Link.txt
    # 694714801 bases of 1055588482 (65.813%) in intersection

    time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \
	galGal6 ZonAlb1) > rbest.log 2>&1 &
    # real	414m13.866s

    cat fb.galGal6.chainRBest.ZonAlb1.txt
    # 720721079 bases of 1055588482 (68.277%) in intersection

#############################################################################
# LASTZ chicken/galGal6 vs American alligator/allMis1 - (DONE - 2018-10-17 - script/hiram)
    mkdir /hive/data/genomes/galGal6/bed/lastzAllMis1.2018-10-17
    cd /hive/data/genomes/galGal6/bed/lastzAllMis1.2018-10-17

   printf "# chicken vs American alligator
# galGal6 vs allMis1
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.00/bin/lastz
BLASTZ_H=2000
BLASTZ_Y=3400
BLASTZ_L=4000
BLASTZ_K=2200
BLASTZ_M=254
BLASTZ_Q=/cluster/data/blastz/HoxD55.q

# TARGET: galGal6 - chicken - Gallus gallus
SEQ1_DIR=/hive/data/genomes/galGal6/galGal6.2bit
SEQ1_LEN=/hive/data/genomes/galGal6/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
SEQ1_LIMIT=40

# QUERY: allMis1 - American alligator - Alligator mississippiensis
SEQ2_DIR=/hive/data/genomes/allMis1/allMis1.2bit
SEQ2_LEN=/hive/data/genomes/allMis1/chrom.sizes
SEQ2_CHUNK=1000000
SEQ2_LIMIT=2000
SEQ2_LAP=0

BASE=/hive/data/genomes/galGal6/bed/lastzAllMis1.2018-10-17
TMPDIR=/dev/shm
" > DEF

    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
      -workhorse=hgwdev -bigClusterHub=ku \
        -dbHost=hgwdev -smallClusterHub=ku \
          -fileServer=hgwdev -syntenicNet) > do.log 2>&1
    # real	368m30.696s

    cat fb.galGal6.chainAllMis1Link.txt
    # 472919428 bases of 1055588482 (44.801%) in intersection

    cat fb.galGal6.chainSynAllMis1Link.txt
    # 394401603 bases of 1055588482 (37.363%) in intersection

    time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \
	galGal6 AllMis1) > rbest.log 2>&1 &
    # real	231m5.251s

    cat fb.galGal6.chainRBest.AllMis1.txt
    # 432775108 bases of 1055588482 (40.998%) in intersection

#############################################################################
# LASTZ chicken/galGal6 vs Chinese alligator/allSin1 - (DONE - 2018-10-17 - script/hiram)
    mkdir /hive/data/genomes/galGal6/bed/lastzAllSin1.2018-10-17
    cd /hive/data/genomes/galGal6/bed/lastzAllSin1.2018-10-17

   printf "# chicken vs Chinese alligator
# galGal6 vs allSin1
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.00/bin/lastz
BLASTZ_H=2000
BLASTZ_Y=3400
BLASTZ_L=4000
BLASTZ_K=2200
BLASTZ_M=254
BLASTZ_Q=/cluster/data/blastz/HoxD55.q

# TARGET: galGal6 - chicken - Gallus gallus
SEQ1_DIR=/hive/data/genomes/galGal6/galGal6.2bit
SEQ1_LEN=/hive/data/genomes/galGal6/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
SEQ1_LIMIT=40

# QUERY: allSin1 - Chinese alligator - Alligator sinensis
SEQ2_DIR=/hive/data/genomes/allSin1/allSin1.2bit
SEQ2_LEN=/hive/data/genomes/allSin1/chrom.sizes
SEQ2_CHUNK=1000000
SEQ2_LIMIT=2000
SEQ2_LAP=0

BASE=/hive/data/genomes/galGal6/bed/lastzAllSin1.2018-10-17
TMPDIR=/dev/shm
" > DEF

    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
      -workhorse=hgwdev -bigClusterHub=ku \
        -dbHost=hgwdev -smallClusterHub=ku \
          -fileServer=hgwdev -syntenicNet) > do.log 2>&1
    # real	393m51.584s

    cat fb.galGal6.chainAllSin1Link.txt
    # 486162994 bases of 1055588482 (46.056%) in intersection

    cat fb.galGal6.chainSynAllSin1Link.txt
    # 406936492 bases of 1055588482 (38.551%) in intersection

    time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \
	galGal6 AllSin1) > rbest.log 2>&1 &
    # real	235m27.827s

    cat fb.galGal6.chainRBest.AllSin1.txt
    # 435270631 bases of 1055588482 (41.235%) in intersection

#############################################################################
# LASTZ chicken/galGal6 vs Parrot/amaVit1 - (DONE - 2018-10-17 - script/hiram)
    mkdir /hive/data/genomes/galGal6/bed/lastzAmaVit1.2018-10-17
    cd /hive/data/genomes/galGal6/bed/lastzAmaVit1.2018-10-17

   printf "# chicken vs Parrot
# galGal6 vs amaVit1
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.00/bin/lastz
BLASTZ_H=2000
BLASTZ_Y=3400
BLASTZ_L=4000
BLASTZ_K=2200
BLASTZ_M=254
BLASTZ_Q=/cluster/data/blastz/HoxD55.q

# TARGET: galGal6 - chicken - Gallus gallus
SEQ1_DIR=/hive/data/genomes/galGal6/galGal6.2bit
SEQ1_LEN=/hive/data/genomes/galGal6/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
SEQ1_LIMIT=40

# QUERY: amaVit1 - Parrot - Amazona vittata
SEQ2_DIR=/hive/data/genomes/amaVit1/amaVit1.2bit
SEQ2_LEN=/hive/data/genomes/amaVit1/chrom.sizes
SEQ2_CHUNK=1000000
SEQ2_LIMIT=2000
SEQ2_LAP=0

BASE=/hive/data/genomes/galGal6/bed/lastzAmaVit1.2018-10-17
TMPDIR=/dev/shm
" > DEF

    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
      -workhorse=hgwdev -bigClusterHub=ku \
        -dbHost=hgwdev -smallClusterHub=ku \
          -fileServer=hgwdev -syntenicNet) > do.log 2>&1
    # real	716m56.681s

    cat fb.galGal6.chainAmaVit1Link.txt
    # 850564670 bases of 1055588482 (80.577%) in intersection

    cat fb.galGal6.chainSynAmaVit1Link.txt
    # 570324827 bases of 1055588482 (54.029%) in intersection

    time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \
	galGal6 AmaVit1) > rbest.log 2>&1 &
    # real	514m10.579s

    cat fb.galGal6.chainRBest.AmaVit1.txt
    # 760058258 bases of 1055588482 (72.003%) in intersection

#############################################################################
# LASTZ chicken/galGal6 vs Mallard duck/anaPla1 - (DONE - 2018-10-17 - script/hiram)
    mkdir /hive/data/genomes/galGal6/bed/lastzAnaPla1.2018-10-17
    cd /hive/data/genomes/galGal6/bed/lastzAnaPla1.2018-10-17

   printf "# chicken vs Mallard duck
# galGal6 vs anaPla1
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.00/bin/lastz
BLASTZ_H=2000
BLASTZ_Y=3400
BLASTZ_L=4000
BLASTZ_K=2200
BLASTZ_M=254
BLASTZ_Q=/cluster/data/blastz/HoxD55.q

# TARGET: galGal6 - chicken - Gallus gallus
SEQ1_DIR=/hive/data/genomes/galGal6/galGal6.2bit
SEQ1_LEN=/hive/data/genomes/galGal6/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
SEQ1_LIMIT=40

# QUERY: anaPla1 - Mallard duck - Anas platyrhynchos
SEQ2_DIR=/hive/data/genomes/anaPla1/anaPla1.2bit
SEQ2_LEN=/hive/data/genomes/anaPla1/chrom.sizes
SEQ2_CHUNK=1000000
SEQ2_LIMIT=2000
SEQ2_LAP=0

BASE=/hive/data/genomes/galGal6/bed/lastzAnaPla1.2018-10-17
TMPDIR=/dev/shm
" > DEF

    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
      -workhorse=hgwdev -bigClusterHub=ku \
        -dbHost=hgwdev -smallClusterHub=ku \
          -fileServer=hgwdev -syntenicNet) > do.log 2>&1
    # real	624m1.292s

    cat fb.galGal6.chainAnaPla1Link.txt
    # 902625137 bases of 1055588482 (85.509%) in intersection

    cat fb.galGal6.chainSynAnaPla1Link.txt
    # 788255126 bases of 1055588482 (74.674%) in intersection

    time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \
	galGal6 AnaPla1) > rbest.log 2>&1 &
    # real	323m11.383s

    cat fb.galGal6.chainRBest.AnaPla1.txt
    # 811001997 bases of 1055588482 (76.829%) in intersection

#############################################################################
# LASTZ chicken/galGal6 vs Lizard/anoCar2 - (DONE - 2018-10-17 - script/hiram)
    mkdir /hive/data/genomes/galGal6/bed/lastzAnoCar2.2018-10-17
    cd /hive/data/genomes/galGal6/bed/lastzAnoCar2.2018-10-17

   printf "# chicken vs Lizard
# galGal6 vs anoCar2
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.00/bin/lastz
BLASTZ_H=2000
BLASTZ_Y=3400
BLASTZ_L=4000
BLASTZ_K=2200
BLASTZ_M=254
BLASTZ_Q=/cluster/data/blastz/HoxD55.q

# TARGET: galGal6 - chicken - Gallus gallus
SEQ1_DIR=/hive/data/genomes/galGal6/galGal6.2bit
SEQ1_LEN=/hive/data/genomes/galGal6/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
SEQ1_LIMIT=40

# QUERY: anoCar2 - Lizard - Anolis carolinensis
SEQ2_DIR=/hive/data/genomes/anoCar2/anoCar2.2bit
SEQ2_LEN=/hive/data/genomes/anoCar2/chrom.sizes
SEQ2_CHUNK=1000000
SEQ2_LIMIT=2000
SEQ2_LAP=0

BASE=/hive/data/genomes/galGal6/bed/lastzAnoCar2.2018-10-17
TMPDIR=/dev/shm
" > DEF

    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
      -workhorse=hgwdev -bigClusterHub=ku \
        -dbHost=hgwdev -smallClusterHub=ku \
          -fileServer=hgwdev -syntenicNet) > do.log 2>&1
    # real	499m17.964s

    cat fb.galGal6.chainAnoCar2Link.txt
    # 153349199 bases of 1055588482 (14.527%) in intersection

    cat fb.galGal6.chainSynAnoCar2Link.txt
    # 93909487 bases of 1055588482 (8.896%) in intersection

    time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \
	galGal6 AnoCar2) > rbest.log 2>&1 &
    # real	378m57.784s

    cat fb.galGal6.chainRBest.AnoCar2.txt
    # 121779211 bases of 1055588482 (11.537%) in intersection

#############################################################################
# LASTZ chicken/galGal6 vs Spiny softshell turtle/apaSpi1 - (DONE - 2018-10-17 - script/hiram)
    mkdir /hive/data/genomes/galGal6/bed/lastzApaSpi1.2018-10-17
    cd /hive/data/genomes/galGal6/bed/lastzApaSpi1.2018-10-17

   printf "# chicken vs Spiny softshell turtle
# galGal6 vs apaSpi1
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.00/bin/lastz
BLASTZ_H=2000
BLASTZ_Y=3400
BLASTZ_L=4000
BLASTZ_K=2200
BLASTZ_M=254
BLASTZ_Q=/cluster/data/blastz/HoxD55.q

# TARGET: galGal6 - chicken - Gallus gallus
SEQ1_DIR=/hive/data/genomes/galGal6/galGal6.2bit
SEQ1_LEN=/hive/data/genomes/galGal6/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
SEQ1_LIMIT=40

# QUERY: apaSpi1 - Spiny softshell turtle - Apalone spinifera
SEQ2_DIR=/hive/data/genomes/apaSpi1/apaSpi1.2bit
SEQ2_LEN=/hive/data/genomes/apaSpi1/chrom.sizes
SEQ2_CHUNK=1000000
SEQ2_LIMIT=2000
SEQ2_LAP=0

BASE=/hive/data/genomes/galGal6/bed/lastzApaSpi1.2018-10-17
TMPDIR=/dev/shm
" > DEF

    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
      -workhorse=hgwdev -bigClusterHub=ku \
        -dbHost=hgwdev -smallClusterHub=ku \
          -fileServer=hgwdev -syntenicNet) > do.log 2>&1
    # real	848m10.616s

    cat fb.galGal6.chainApaSpi1Link.txt
    # 405079543 bases of 1055588482 (38.375%) in intersection

    cat fb.galGal6.chainSynApaSpi1Link.txt
    # 73623886 bases of 1055588482 (6.975%) in intersection

    time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \
	galGal6 ApaSpi1) > rbest.log 2>&1 &
    # real	635m31.914s

    cat fb.galGal6.chainRBest.ApaSpi1.txt
    # 345975149 bases of 1055588482 (32.776%) in intersection

#############################################################################
# LASTZ chicken/galGal6 vs Bar tailed trogon/apaVit1 - (DONE - 2018-10-17 - script/hiram)
    mkdir /hive/data/genomes/galGal6/bed/lastzApaVit1.2018-10-17
    cd /hive/data/genomes/galGal6/bed/lastzApaVit1.2018-10-17

   printf "# chicken vs Bar tailed trogon
# galGal6 vs apaVit1
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.00/bin/lastz
BLASTZ_H=2000
BLASTZ_Y=3400
BLASTZ_L=4000
BLASTZ_K=2200
BLASTZ_M=254
BLASTZ_Q=/cluster/data/blastz/HoxD55.q

# TARGET: galGal6 - chicken - Gallus gallus
SEQ1_DIR=/hive/data/genomes/galGal6/galGal6.2bit
SEQ1_LEN=/hive/data/genomes/galGal6/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
SEQ1_LIMIT=40

# QUERY: apaVit1 - Bar tailed trogon - Apaloderma vittatum
SEQ2_DIR=/hive/data/genomes/apaVit1/apaVit1.2bit
SEQ2_LEN=/hive/data/genomes/apaVit1/chrom.sizes
SEQ2_CHUNK=1000000
SEQ2_LIMIT=2000
SEQ2_LAP=0

BASE=/hive/data/genomes/galGal6/bed/lastzApaVit1.2018-10-17
TMPDIR=/dev/shm
" > DEF

    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
      -workhorse=hgwdev -bigClusterHub=ku \
        -dbHost=hgwdev -smallClusterHub=ku \
          -fileServer=hgwdev -syntenicNet) > do.log 2>&1
    # real	666m21.837s

    cat fb.galGal6.chainApaVit1Link.txt
    # 855130988 bases of 1055588482 (81.010%) in intersection

    cat fb.galGal6.chainSynApaVit1Link.txt
    # 707907699 bases of 1055588482 (67.063%) in intersection

    time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \
	galGal6 ApaVit1) > rbest.log 2>&1 &
    # real	395m8.109s

    cat fb.galGal6.chainRBest.ApaVit1.txt
    # 768399443 bases of 1055588482 (72.793%) in intersection

#############################################################################
# LASTZ chicken/galGal6 vs Emperor penguin/aptFor1 - (DONE - 2018-10-17 - script/hiram)
    mkdir /hive/data/genomes/galGal6/bed/lastzAptFor1.2018-10-17
    cd /hive/data/genomes/galGal6/bed/lastzAptFor1.2018-10-17

   printf "# chicken vs Emperor penguin
# galGal6 vs aptFor1
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.00/bin/lastz
BLASTZ_H=2000
BLASTZ_Y=3400
BLASTZ_L=4000
BLASTZ_K=2200
BLASTZ_M=254
BLASTZ_Q=/cluster/data/blastz/HoxD55.q

# TARGET: galGal6 - chicken - Gallus gallus
SEQ1_DIR=/hive/data/genomes/galGal6/galGal6.2bit
SEQ1_LEN=/hive/data/genomes/galGal6/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
SEQ1_LIMIT=40

# QUERY: aptFor1 - Emperor penguin - Aptenodytes forsteri
SEQ2_DIR=/hive/data/genomes/aptFor1/aptFor1.2bit
SEQ2_LEN=/hive/data/genomes/aptFor1/chrom.sizes
SEQ2_CHUNK=1000000
SEQ2_LIMIT=2000
SEQ2_LAP=0

BASE=/hive/data/genomes/galGal6/bed/lastzAptFor1.2018-10-17
TMPDIR=/dev/shm
" > DEF

    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
      -workhorse=hgwdev -bigClusterHub=ku \
        -dbHost=hgwdev -smallClusterHub=ku \
          -fileServer=hgwdev -syntenicNet) > do.log 2>&1
    # real	482m48.347s

    cat fb.galGal6.chainAptFor1Link.txt
    # 916608502 bases of 1055588482 (86.834%) in intersection

    cat fb.galGal6.chainSynAptFor1Link.txt
    # 828156085 bases of 1055588482 (78.454%) in intersection

    time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \
	galGal6 AptFor1) > rbest.log 2>&1 &
    # real	222m3.219s

    cat fb.galGal6.chainRBest.AptFor1.txt
    # 840254605 bases of 1055588482 (79.601%) in intersection

#############################################################################
# LASTZ chicken/galGal6 vs Golden eagle/aquChr2 - (DONE - 2018-10-17 - script/hiram)
    mkdir /hive/data/genomes/galGal6/bed/lastzAquChr2.2018-10-17
    cd /hive/data/genomes/galGal6/bed/lastzAquChr2.2018-10-17

   printf "# chicken vs Golden eagle
# galGal6 vs aquChr2
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.00/bin/lastz
BLASTZ_H=2000
BLASTZ_Y=3400
BLASTZ_L=4000
BLASTZ_K=2200
BLASTZ_M=254
BLASTZ_Q=/cluster/data/blastz/HoxD55.q

# TARGET: galGal6 - chicken - Gallus gallus
SEQ1_DIR=/hive/data/genomes/galGal6/galGal6.2bit
SEQ1_LEN=/hive/data/genomes/galGal6/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
SEQ1_LIMIT=40

# QUERY: aquChr2 - Golden eagle - Aquila chrysaetos canadensis
SEQ2_DIR=/hive/data/genomes/aquChr2/aquChr2.2bit
SEQ2_LEN=/hive/data/genomes/aquChr2/chrom.sizes
SEQ2_CHUNK=1000000
SEQ2_LIMIT=2000
SEQ2_LAP=0

BASE=/hive/data/genomes/galGal6/bed/lastzAquChr2.2018-10-17
TMPDIR=/dev/shm
" > DEF

    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
      -workhorse=hgwdev -bigClusterHub=ku \
        -dbHost=hgwdev -smallClusterHub=ku \
          -fileServer=hgwdev -syntenicNet) > do.log 2>&1
    # real	446m55.621s

    cat fb.galGal6.chainAquChr2Link.txt
    # 925613456 bases of 1055588482 (87.687%) in intersection

    cat fb.galGal6.chainSynAquChr2Link.txt
    # 831330877 bases of 1055588482 (78.755%) in intersection

    time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \
	galGal6 AquChr2) > rbest.log 2>&1 &
    # real	232m0.358s

    cat fb.galGal6.chainRBest.AquChr2.txt
    # 848365224 bases of 1055588482 (80.369%) in intersection

#############################################################################
# LASTZ chicken/galGal6 vs Scarlet macaw/araMac1 - (DONE - 2018-10-17 - script/hiram)
    mkdir /hive/data/genomes/galGal6/bed/lastzAraMac1.2018-10-17
    cd /hive/data/genomes/galGal6/bed/lastzAraMac1.2018-10-17

   printf "# chicken vs Scarlet macaw
# galGal6 vs araMac1
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.00/bin/lastz
BLASTZ_H=2000
BLASTZ_Y=3400
BLASTZ_L=4000
BLASTZ_K=2200
BLASTZ_M=254
BLASTZ_Q=/cluster/data/blastz/HoxD55.q

# TARGET: galGal6 - chicken - Gallus gallus
SEQ1_DIR=/hive/data/genomes/galGal6/galGal6.2bit
SEQ1_LEN=/hive/data/genomes/galGal6/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
SEQ1_LIMIT=40

# QUERY: araMac1 - Scarlet macaw - Ara macao
SEQ2_DIR=/hive/data/genomes/araMac1/araMac1.2bit
SEQ2_LEN=/hive/data/genomes/araMac1/chrom.sizes
SEQ2_CHUNK=1000000
SEQ2_LIMIT=2000
SEQ2_LAP=0

BASE=/hive/data/genomes/galGal6/bed/lastzAraMac1.2018-10-17
TMPDIR=/dev/shm
" > DEF

    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
      -workhorse=hgwdev -bigClusterHub=ku \
        -dbHost=hgwdev -smallClusterHub=ku \
          -fileServer=hgwdev -syntenicNet) > do.log 2>&1
    # real	890m2.745s

    cat fb.galGal6.chainAraMac1Link.txt
    # 804150969 bases of 1055588482 (76.180%) in intersection

    cat fb.galGal6.chainSynAraMac1Link.txt
    # 463740960 bases of 1055588482 (43.932%) in intersection

    time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \
	galGal6 AraMac1) > rbest.log 2>&1 &
    # real	640m35.617s

    cat fb.galGal6.chainRBest.AraMac1.txt
    # 708288676 bases of 1055588482 (67.099%) in intersection

#############################################################################
# LASTZ chicken/galGal6 vs Crowned crain/balPav1 - (DONE - 2018-10-17 - script/hiram)
    mkdir /hive/data/genomes/galGal6/bed/lastzBalPav1.2018-10-17
    cd /hive/data/genomes/galGal6/bed/lastzBalPav1.2018-10-17

   printf "# chicken vs Crowned crain
# galGal6 vs balPav1
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.00/bin/lastz
BLASTZ_H=2000
BLASTZ_Y=3400
BLASTZ_L=4000
BLASTZ_K=2200
BLASTZ_M=254
BLASTZ_Q=/cluster/data/blastz/HoxD55.q

# TARGET: galGal6 - chicken - Gallus gallus
SEQ1_DIR=/hive/data/genomes/galGal6/galGal6.2bit
SEQ1_LEN=/hive/data/genomes/galGal6/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
SEQ1_LIMIT=40

# QUERY: balPav1 - Crowned crain - Balearica pavonina gibbericeps
SEQ2_DIR=/hive/data/genomes/balPav1/balPav1.2bit
SEQ2_LEN=/hive/data/genomes/balPav1/chrom.sizes
SEQ2_CHUNK=1000000
SEQ2_LIMIT=2000
SEQ2_LAP=0

BASE=/hive/data/genomes/galGal6/bed/lastzBalPav1.2018-10-17
TMPDIR=/dev/shm
" > DEF

    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
      -workhorse=hgwdev -bigClusterHub=ku \
        -dbHost=hgwdev -smallClusterHub=ku \
          -fileServer=hgwdev -syntenicNet) > do.log 2>&1
    # real	520m25.509s

    cat fb.galGal6.chainBalPav1Link.txt
    # 893943891 bases of 1055588482 (84.687%) in intersection

    cat fb.galGal6.chainSynBalPav1Link.txt
    # 760199826 bases of 1055588482 (72.017%) in intersection

    time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \
	galGal6 BalPav1) > rbest.log 2>&1 &
    # real	317m39.665s

    cat fb.galGal6.chainRBest.BalPav1.txt
    # 816345959 bases of 1055588482 (77.336%) in intersection

#############################################################################
# LASTZ chicken/galGal6 vs Rhinoceros hornbill/bucRhi1 - (DONE - 2018-10-17 - script/hiram)
    mkdir /hive/data/genomes/galGal6/bed/lastzBucRhi1.2018-10-17
    cd /hive/data/genomes/galGal6/bed/lastzBucRhi1.2018-10-17

   printf "# chicken vs Rhinoceros hornbill
# galGal6 vs bucRhi1
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.00/bin/lastz
BLASTZ_H=2000
BLASTZ_Y=3400
BLASTZ_L=4000
BLASTZ_K=2200
BLASTZ_M=254
BLASTZ_Q=/cluster/data/blastz/HoxD55.q

# TARGET: galGal6 - chicken - Gallus gallus
SEQ1_DIR=/hive/data/genomes/galGal6/galGal6.2bit
SEQ1_LEN=/hive/data/genomes/galGal6/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
SEQ1_LIMIT=40

# QUERY: bucRhi1 - Rhinoceros hornbill - Buceros rhinoceros silvestris
SEQ2_DIR=/hive/data/genomes/bucRhi1/bucRhi1.2bit
SEQ2_LEN=/hive/data/genomes/bucRhi1/chrom.sizes
SEQ2_CHUNK=1000000
SEQ2_LIMIT=2000
SEQ2_LAP=0

BASE=/hive/data/genomes/galGal6/bed/lastzBucRhi1.2018-10-17
TMPDIR=/dev/shm
" > DEF

    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
      -workhorse=hgwdev -bigClusterHub=ku \
        -dbHost=hgwdev -smallClusterHub=ku \
          -fileServer=hgwdev -syntenicNet) > do.log 2>&1
    # real	621m43.314s

    cat fb.galGal6.chainBucRhi1Link.txt
    # 853039041 bases of 1055588482 (80.812%) in intersection

    cat fb.galGal6.chainSynBucRhi1Link.txt
    # 702565404 bases of 1055588482 (66.557%) in intersection

    time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \
	galGal6 BucRhi1) > rbest.log 2>&1 &
    # real	409m2.624s

    cat fb.galGal6.chainRBest.BucRhi1.txt
    # 762575881 bases of 1055588482 (72.242%) in intersection

#############################################################################
# LASTZ chicken/galGal6 vs Anna's hummingbird/calAnn1 - (DONE - 2018-10-17 - script/hiram)
    mkdir /hive/data/genomes/galGal6/bed/lastzCalAnn1.2018-10-17
    cd /hive/data/genomes/galGal6/bed/lastzCalAnn1.2018-10-17

   printf "# chicken vs Anna's hummingbird
# galGal6 vs calAnn1
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.00/bin/lastz
BLASTZ_H=2000
BLASTZ_Y=3400
BLASTZ_L=4000
BLASTZ_K=2200
BLASTZ_M=254
BLASTZ_Q=/cluster/data/blastz/HoxD55.q

# TARGET: galGal6 - chicken - Gallus gallus
SEQ1_DIR=/hive/data/genomes/galGal6/galGal6.2bit
SEQ1_LEN=/hive/data/genomes/galGal6/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
SEQ1_LIMIT=40

# QUERY: calAnn1 - Anna's hummingbird - Calypte anna
SEQ2_DIR=/hive/data/genomes/calAnn1/calAnn1.2bit
SEQ2_LEN=/hive/data/genomes/calAnn1/chrom.sizes
SEQ2_CHUNK=1000000
SEQ2_LIMIT=2000
SEQ2_LAP=0

BASE=/hive/data/genomes/galGal6/bed/lastzCalAnn1.2018-10-17
TMPDIR=/dev/shm
" > DEF

    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
      -workhorse=hgwdev -bigClusterHub=ku \
        -dbHost=hgwdev -smallClusterHub=ku \
          -fileServer=hgwdev -syntenicNet) > do.log 2>&1
    # real	645m42.059s

    cat fb.galGal6.chainCalAnn1Link.txt
    # 841653301 bases of 1055588482 (79.733%) in intersection

    cat fb.galGal6.chainSynCalAnn1Link.txt
    # 708340584 bases of 1055588482 (67.104%) in intersection

    time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \
	galGal6 CalAnn1) > rbest.log 2>&1 &
    # real	402m36.129s

    cat fb.galGal6.chainRBest.CalAnn1.txt
    # 736578452 bases of 1055588482 (69.779%) in intersection

#############################################################################
# LASTZ chicken/galGal6 vs Chuck-will's-widow/capCar1 - (DONE - 2018-10-17 - script/hiram)
    mkdir /hive/data/genomes/galGal6/bed/lastzCapCar1.2018-10-17
    cd /hive/data/genomes/galGal6/bed/lastzCapCar1.2018-10-17

   printf "# chicken vs Chuck-will's-widow
# galGal6 vs capCar1
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.00/bin/lastz
BLASTZ_H=2000
BLASTZ_Y=3400
BLASTZ_L=4000
BLASTZ_K=2200
BLASTZ_M=254
BLASTZ_Q=/cluster/data/blastz/HoxD55.q

# TARGET: galGal6 - chicken - Gallus gallus
SEQ1_DIR=/hive/data/genomes/galGal6/galGal6.2bit
SEQ1_LEN=/hive/data/genomes/galGal6/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
SEQ1_LIMIT=40

# QUERY: capCar1 - Chuck-will's-widow - Caprimulgus carolinensis
SEQ2_DIR=/hive/data/genomes/capCar1/capCar1.2bit
SEQ2_LEN=/hive/data/genomes/capCar1/chrom.sizes
SEQ2_CHUNK=1000000
SEQ2_LIMIT=2000
SEQ2_LAP=0

BASE=/hive/data/genomes/galGal6/bed/lastzCapCar1.2018-10-17
TMPDIR=/dev/shm
" > DEF

    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
      -workhorse=hgwdev -bigClusterHub=ku \
        -dbHost=hgwdev -smallClusterHub=ku \
          -fileServer=hgwdev -syntenicNet) > do.log 2>&1
    # real	618m38.832s

    cat fb.galGal6.chainCapCar1Link.txt
    # 882181787 bases of 1055588482 (83.573%) in intersection

    cat fb.galGal6.chainSynCapCar1Link.txt
    # 724094046 bases of 1055588482 (68.596%) in intersection

    time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \
	galGal6 CapCar1) > rbest.log 2>&1 &
    # real	404m29.064s

    cat fb.galGal6.chainRBest.CapCar1.txt
    # 795678181 bases of 1055588482 (75.378%) in intersection

#############################################################################
# LASTZ chicken/galGal6 vs Zebrafish/danRer11 - (DONE - 2018-10-17 - script/hiram)
    mkdir /hive/data/genomes/galGal6/bed/lastzDanRer11.2018-10-17
    cd /hive/data/genomes/galGal6/bed/lastzDanRer11.2018-10-17

   printf "# chicken vs Zebrafish
# galGal6 vs danRer11
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.00/bin/lastz
BLASTZ_H=2000
BLASTZ_Y=3400
BLASTZ_L=4000
BLASTZ_K=2200
BLASTZ_M=254
BLASTZ_Q=/cluster/data/blastz/HoxD55.q

# TARGET: galGal6 - chicken - Gallus gallus
SEQ1_DIR=/hive/data/genomes/galGal6/galGal6.2bit
SEQ1_LEN=/hive/data/genomes/galGal6/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
SEQ1_LIMIT=40

# QUERY: danRer11 - Zebrafish - Danio rerio
SEQ2_DIR=/hive/data/genomes/danRer11/danRer11.2bit
SEQ2_LEN=/hive/data/genomes/danRer11/chrom.sizes
SEQ2_CHUNK=1000000
SEQ2_LIMIT=2000
SEQ2_LAP=0

BASE=/hive/data/genomes/galGal6/bed/lastzDanRer11.2018-10-17
TMPDIR=/dev/shm
" > DEF

    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
      -workhorse=hgwdev -bigClusterHub=ku \
        -dbHost=hgwdev -smallClusterHub=ku \
          -fileServer=hgwdev -syntenicNet) > do.log 2>&1
    # real	288m51.949s

    cat fb.galGal6.chainDanRer11Link.txt
    # 67051784 bases of 1055588482 (6.352%) in intersection

    cat fb.galGal6.chainSynDanRer11Link.txt
    # 15220724 bases of 1055588482 (1.442%) in intersection

    time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \
	galGal6 DanRer11) > rbest.log 2>&1 &
    # real	181m30.518s

    cat fb.galGal6.chainRBest.DanRer11.txt
    # 54875577 bases of 1055588482 (5.199%) in intersection

#############################################################################
# LASTZ chicken/galGal6 vs Collared flycatcher/ficAlb2 - (DONE - 2018-10-17 - script/hiram)
    mkdir /hive/data/genomes/galGal6/bed/lastzFicAlb2.2018-10-17
    cd /hive/data/genomes/galGal6/bed/lastzFicAlb2.2018-10-17

   printf "# chicken vs Collared flycatcher
# galGal6 vs ficAlb2
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.00/bin/lastz
BLASTZ_H=2000
BLASTZ_Y=3400
BLASTZ_L=4000
BLASTZ_K=2200
BLASTZ_M=254
BLASTZ_Q=/cluster/data/blastz/HoxD55.q

# TARGET: galGal6 - chicken - Gallus gallus
SEQ1_DIR=/hive/data/genomes/galGal6/galGal6.2bit
SEQ1_LEN=/hive/data/genomes/galGal6/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
SEQ1_LIMIT=40

# QUERY: ficAlb2 - Collared flycatcher - Ficedula albicollis
SEQ2_DIR=/hive/data/genomes/ficAlb2/ficAlb2.2bit
SEQ2_LEN=/hive/data/genomes/ficAlb2/chrom.sizes
SEQ2_CHUNK=1000000
SEQ2_LIMIT=2000
SEQ2_LAP=0

BASE=/hive/data/genomes/galGal6/bed/lastzFicAlb2.2018-10-17
TMPDIR=/dev/shm
" > DEF

    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
      -workhorse=hgwdev -bigClusterHub=ku \
        -dbHost=hgwdev -smallClusterHub=ku \
          -fileServer=hgwdev -syntenicNet) > do.log 2>&1
    # real	916m56.403s

    cat fb.galGal6.chainFicAlb2Link.txt
    # 837654801 bases of 1055588482 (79.354%) in intersection

    cat fb.galGal6.chainSynFicAlb2Link.txt
    # 701981619 bases of 1055588482 (66.501%) in intersection

    time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \
	galGal6 FicAlb2) > rbest.log 2>&1 &
    # real	687m21.884s

    cat fb.galGal6.chainRBest.FicAlb2.txt
    # 733810856 bases of 1055588482 (69.517%) in intersection

#############################################################################
# LASTZ chicken/galGal6 vs Fugu/fr3 - (DONE - 2018-10-17 - script/hiram)
    mkdir /hive/data/genomes/galGal6/bed/lastzFr3.2018-10-17
    cd /hive/data/genomes/galGal6/bed/lastzFr3.2018-10-17

   printf "# chicken vs Fugu
# galGal6 vs fr3
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.00/bin/lastz
BLASTZ_H=2000
BLASTZ_Y=3400
BLASTZ_L=4000
BLASTZ_K=2200
BLASTZ_M=254
BLASTZ_Q=/cluster/data/blastz/HoxD55.q

# TARGET: galGal6 - chicken - Gallus gallus
SEQ1_DIR=/hive/data/genomes/galGal6/galGal6.2bit
SEQ1_LEN=/hive/data/genomes/galGal6/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
SEQ1_LIMIT=40

# QUERY: fr3 - Fugu - Takifugu rubripes
SEQ2_DIR=/hive/data/genomes/fr3/fr3.2bit
SEQ2_LEN=/hive/data/genomes/fr3/chrom.sizes
SEQ2_CHUNK=1000000
SEQ2_LIMIT=2000
SEQ2_LAP=0

BASE=/hive/data/genomes/galGal6/bed/lastzFr3.2018-10-17
TMPDIR=/dev/shm
" > DEF

    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
      -workhorse=hgwdev -bigClusterHub=ku \
        -dbHost=hgwdev -smallClusterHub=ku \
          -fileServer=hgwdev -syntenicNet) > do.log 2>&1
    # real	89m47.854s

    cat fb.galGal6.chainFr3Link.txt
    # 42301582 bases of 1055588482 (4.007%) in intersection

    cat fb.galGal6.chainSynFr3Link.txt
    # 11843090 bases of 1055588482 (1.122%) in intersection

    time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \
	galGal6 Fr3) > rbest.log 2>&1 &
    # real	56m3.102s

    cat fb.galGal6.chainRBest.Fr3.txt
    # 33236371 bases of 1055588482 (3.149%) in intersection

#############################################################################
# LASTZ chicken/galGal6 vs Zebra finch/taeGut2 - (DONE - 2018-10-17 - script/hiram)
    mkdir /hive/data/genomes/galGal6/bed/lastzTaeGut2.2018-10-17
    cd /hive/data/genomes/galGal6/bed/lastzTaeGut2.2018-10-17

   printf "# chicken vs Zebra finch
# galGal6 vs taeGut2
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.00/bin/lastz
BLASTZ_H=2000
BLASTZ_Y=3400
BLASTZ_L=4000
BLASTZ_K=2200
BLASTZ_M=254
BLASTZ_Q=/cluster/data/blastz/HoxD55.q

# TARGET: galGal6 - chicken - Gallus gallus
SEQ1_DIR=/hive/data/genomes/galGal6/galGal6.2bit
SEQ1_LEN=/hive/data/genomes/galGal6/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
SEQ1_LIMIT=40

# QUERY: taeGut2 - Zebra finch - Taeniopygia guttata
SEQ2_DIR=/hive/data/genomes/taeGut2/taeGut2.2bit
SEQ2_LEN=/hive/data/genomes/taeGut2/chrom.sizes
SEQ2_CHUNK=1000000
SEQ2_LIMIT=2000
SEQ2_LAP=0

BASE=/hive/data/genomes/galGal6/bed/lastzTaeGut2.2018-10-17
TMPDIR=/dev/shm
" > DEF

    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
      -workhorse=hgwdev -bigClusterHub=ku \
        -dbHost=hgwdev -smallClusterHub=ku \
          -fileServer=hgwdev -syntenicNet) > do.log 2>&1
    # real	483m53.121s

    cat fb.galGal6.chainTaeGut2Link.txt
    # 781017086 bases of 1055588482 (73.989%) in intersection

    cat fb.galGal6.chainSynTaeGut2Link.txt
    # 692861685 bases of 1055588482 (65.637%) in intersection

    time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \
	galGal6 TaeGut2) > rbest.log 2>&1 &
    # real	333m5.501s

    cat fb.galGal6.chainRBest.TaeGut2.txt
    # 718742085 bases of 1055588482 (68.089%) in intersection

#############################################################################
# LASTZ chicken/galGal6 vs Tetraodon/tetNig1 - (DONE - 2018-10-17 - script/hiram)
    mkdir /hive/data/genomes/galGal6/bed/lastzTetNig1.2018-10-17
    cd /hive/data/genomes/galGal6/bed/lastzTetNig1.2018-10-17

   printf "# chicken vs Tetraodon
# galGal6 vs tetNig1
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.00/bin/lastz
BLASTZ_H=2000
BLASTZ_Y=3400
BLASTZ_L=4000
BLASTZ_K=2200
BLASTZ_M=254
BLASTZ_Q=/cluster/data/blastz/HoxD55.q

# TARGET: galGal6 - chicken - Gallus gallus
SEQ1_DIR=/hive/data/genomes/galGal6/galGal6.2bit
SEQ1_LEN=/hive/data/genomes/galGal6/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
SEQ1_LIMIT=40

# QUERY: tetNig1 - Tetraodon - Tetraodon nigroviridis
SEQ2_DIR=/hive/data/genomes/tetNig1/tetNig1.2bit
SEQ2_LEN=/hive/data/genomes/tetNig1/chrom.sizes
SEQ2_CHUNK=1000000
SEQ2_LIMIT=2000
SEQ2_LAP=0

BASE=/hive/data/genomes/galGal6/bed/lastzTetNig1.2018-10-17
TMPDIR=/dev/shm
" > DEF

    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
      -workhorse=hgwdev -bigClusterHub=ku \
        -dbHost=hgwdev -smallClusterHub=ku \
          -fileServer=hgwdev -syntenicNet) > do.log 2>&1
    # real	146m39.394s

    cat fb.galGal6.chainTetNig1Link.txt
    # 50235405 bases of 1055588482 (4.759%) in intersection

    cat fb.galGal6.chainSynTetNig1Link.txt
    # 11303688 bases of 1055588482 (1.071%) in intersection

    time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \
	galGal6 TetNig1) > rbest.log 2>&1 &
    # real	125m11.284s

    cat fb.galGal6.chainRBest.TetNig1.txt
    # 36506176 bases of 1055588482 (3.458%) in intersection

#############################################################################
# LASTZ chicken/galGal6 vs White throated tinamou/tinGut2 - (DONE - 2018-10-17 - script/hiram)
    mkdir /hive/data/genomes/galGal6/bed/lastzTinGut2.2018-10-17
    cd /hive/data/genomes/galGal6/bed/lastzTinGut2.2018-10-17

   printf "# chicken vs White throated tinamou
# galGal6 vs tinGut2
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.00/bin/lastz
BLASTZ_H=2000
BLASTZ_Y=3400
BLASTZ_L=4000
BLASTZ_K=2200
BLASTZ_M=254
BLASTZ_Q=/cluster/data/blastz/HoxD55.q

# TARGET: galGal6 - chicken - Gallus gallus
SEQ1_DIR=/hive/data/genomes/galGal6/galGal6.2bit
SEQ1_LEN=/hive/data/genomes/galGal6/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
SEQ1_LIMIT=40

# QUERY: tinGut2 - White throated tinamou - Tinamus guttatus
SEQ2_DIR=/hive/data/genomes/tinGut2/tinGut2.2bit
SEQ2_LEN=/hive/data/genomes/tinGut2/chrom.sizes
SEQ2_CHUNK=1000000
SEQ2_LIMIT=2000
SEQ2_LAP=0

BASE=/hive/data/genomes/galGal6/bed/lastzTinGut2.2018-10-17
TMPDIR=/dev/shm
" > DEF

    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
      -workhorse=hgwdev -bigClusterHub=ku \
        -dbHost=hgwdev -smallClusterHub=ku \
          -fileServer=hgwdev -syntenicNet) > do.log 2>&1
    # real	389m18.202s

    cat fb.galGal6.chainTinGut2Link.txt
    # 776674866 bases of 1055588482 (73.577%) in intersection

    cat fb.galGal6.chainSynTinGut2Link.txt
    # 660844755 bases of 1055588482 (62.604%) in intersection

    time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \
	galGal6 TinGut2) > rbest.log 2>&1 &
    # real	285m22.493s

    cat fb.galGal6.chainRBest.TinGut2.txt
    # 688296692 bases of 1055588482 (65.205%) in intersection

#############################################################################
# LASTZ chicken/galGal6 vs X. tropicalis/xenTro9 - (DONE - 2018-10-17 - script/hiram)
    mkdir /hive/data/genomes/galGal6/bed/lastzXenTro9.2018-10-17
    cd /hive/data/genomes/galGal6/bed/lastzXenTro9.2018-10-17

   printf "# chicken vs X. tropicalis
# galGal6 vs xenTro9
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.00/bin/lastz
BLASTZ_H=2000
BLASTZ_Y=3400
BLASTZ_L=4000
BLASTZ_K=2200
BLASTZ_M=254
BLASTZ_Q=/cluster/data/blastz/HoxD55.q

# TARGET: galGal6 - chicken - Gallus gallus
SEQ1_DIR=/hive/data/genomes/galGal6/galGal6.2bit
SEQ1_LEN=/hive/data/genomes/galGal6/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
SEQ1_LIMIT=40

# QUERY: xenTro9 - X. tropicalis - Xenopus tropicalis
SEQ2_DIR=/hive/data/genomes/xenTro9/xenTro9.2bit
SEQ2_LEN=/hive/data/genomes/xenTro9/chrom.sizes
SEQ2_CHUNK=1000000
SEQ2_LIMIT=2000
SEQ2_LAP=0

BASE=/hive/data/genomes/galGal6/bed/lastzXenTro9.2018-10-17
TMPDIR=/dev/shm
" > DEF

    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
      -workhorse=hgwdev -bigClusterHub=ku \
        -dbHost=hgwdev -smallClusterHub=ku \
          -fileServer=hgwdev -syntenicNet) > do.log 2>&1
    # real	359m38.252s

    cat fb.galGal6.chainXenTro9Link.txt
    # 85528839 bases of 1055588482 (8.102%) in intersection

    cat fb.galGal6.chainSynXenTro9Link.txt
    # 41958665 bases of 1055588482 (3.975%) in intersection

    time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \
	galGal6 XenTro9) > rbest.log 2>&1 &
    # real	250m49.764s

    cat fb.galGal6.chainRBest.XenTro9.txt
    # 66190094 bases of 1055588482 (6.270%) in intersection

#############################################################################
# LASTZ chicken/galGal6 vs Red-legged seriema/carCri1 - (DONE - 2018-10-18 - script/hiram)
    mkdir /hive/data/genomes/galGal6/bed/lastzCarCri1.2018-10-18
    cd /hive/data/genomes/galGal6/bed/lastzCarCri1.2018-10-18

   printf "# chicken vs Red-legged seriema
# galGal6 vs carCri1
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.00/bin/lastz
BLASTZ_H=2000
BLASTZ_Y=3400
BLASTZ_L=4000
BLASTZ_K=2200
BLASTZ_M=254
BLASTZ_Q=/cluster/data/blastz/HoxD55.q

# TARGET: galGal6 - chicken - Gallus gallus
SEQ1_DIR=/hive/data/genomes/galGal6/galGal6.2bit
SEQ1_LEN=/hive/data/genomes/galGal6/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
SEQ1_LIMIT=40

# QUERY: carCri1 - Red-legged seriema - Cariama cristata
SEQ2_DIR=/hive/data/genomes/carCri1/carCri1.2bit
SEQ2_LEN=/hive/data/genomes/carCri1/chrom.sizes
SEQ2_CHUNK=1000000
SEQ2_LIMIT=2000
SEQ2_LAP=0

BASE=/hive/data/genomes/galGal6/bed/lastzCarCri1.2018-10-18
TMPDIR=/dev/shm
" > DEF

    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
      -workhorse=hgwdev -bigClusterHub=ku \
        -dbHost=hgwdev -smallClusterHub=ku \
          -fileServer=hgwdev -syntenicNet) > do.log 2>&1
    # real	477m19.869s

    cat fb.galGal6.chainCarCri1Link.txt
    # 898243255 bases of 1055588482 (85.094%) in intersection

    cat fb.galGal6.chainSynCarCri1Link.txt
    # 766895002 bases of 1055588482 (72.651%) in intersection

    time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \
	galGal6 CarCri1) > rbest.log 2>&1 &
    # real	340m49.453s

    cat fb.galGal6.chainRBest.CarCri1.txt
    # 818808423 bases of 1055588482 (77.569%) in intersection

#############################################################################
# LASTZ chicken/galGal6 vs Killdeer/chaVoc2 - (DONE - 2018-10-18 - script/hiram)
    mkdir /hive/data/genomes/galGal6/bed/lastzChaVoc2.2018-10-18
    cd /hive/data/genomes/galGal6/bed/lastzChaVoc2.2018-10-18

   printf "# chicken vs Killdeer
# galGal6 vs chaVoc2
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.00/bin/lastz
BLASTZ_H=2000
BLASTZ_Y=3400
BLASTZ_L=4000
BLASTZ_K=2200
BLASTZ_M=254
BLASTZ_Q=/cluster/data/blastz/HoxD55.q

# TARGET: galGal6 - chicken - Gallus gallus
SEQ1_DIR=/hive/data/genomes/galGal6/galGal6.2bit
SEQ1_LEN=/hive/data/genomes/galGal6/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
SEQ1_LIMIT=40

# QUERY: chaVoc2 - Killdeer - Charadrius vociferus
SEQ2_DIR=/hive/data/genomes/chaVoc2/chaVoc2.2bit
SEQ2_LEN=/hive/data/genomes/chaVoc2/chrom.sizes
SEQ2_CHUNK=1000000
SEQ2_LIMIT=2000
SEQ2_LAP=0

BASE=/hive/data/genomes/galGal6/bed/lastzChaVoc2.2018-10-18
TMPDIR=/dev/shm
" > DEF

    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
      -workhorse=hgwdev -bigClusterHub=ku \
        -dbHost=hgwdev -smallClusterHub=ku \
          -fileServer=hgwdev -syntenicNet) > do.log 2>&1
    # real	421m52.748s

    cat fb.galGal6.chainChaVoc2Link.txt
    # 910629364 bases of 1055588482 (86.267%) in intersection

    cat fb.galGal6.chainSynChaVoc2Link.txt
    # 813864162 bases of 1055588482 (77.101%) in intersection

    time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \
	galGal6 ChaVoc2) > rbest.log 2>&1 &
    # real	242m34.087s

    cat fb.galGal6.chainRBest.ChaVoc2.txt
    # 833063294 bases of 1055588482 (78.919%) in intersection

#############################################################################
# LASTZ chicken/galGal6 vs Green seaturtle/cheMyd1 - (DONE - 2018-10-18 - script/hiram)
    mkdir /hive/data/genomes/galGal6/bed/lastzCheMyd1.2018-10-18
    cd /hive/data/genomes/galGal6/bed/lastzCheMyd1.2018-10-18

   printf "# chicken vs Green seaturtle
# galGal6 vs cheMyd1
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.00/bin/lastz
BLASTZ_H=2000
BLASTZ_Y=3400
BLASTZ_L=4000
BLASTZ_K=2200
BLASTZ_M=254
BLASTZ_Q=/cluster/data/blastz/HoxD55.q

# TARGET: galGal6 - chicken - Gallus gallus
SEQ1_DIR=/hive/data/genomes/galGal6/galGal6.2bit
SEQ1_LEN=/hive/data/genomes/galGal6/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
SEQ1_LIMIT=40

# QUERY: cheMyd1 - Green seaturtle - Chelonia mydas
SEQ2_DIR=/hive/data/genomes/cheMyd1/cheMyd1.2bit
SEQ2_LEN=/hive/data/genomes/cheMyd1/chrom.sizes
SEQ2_CHUNK=1000000
SEQ2_LIMIT=2000
SEQ2_LAP=0

BASE=/hive/data/genomes/galGal6/bed/lastzCheMyd1.2018-10-18
TMPDIR=/dev/shm
" > DEF

    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
      -workhorse=hgwdev -bigClusterHub=ku \
        -dbHost=hgwdev -smallClusterHub=ku \
          -fileServer=hgwdev -syntenicNet) > do.log 2>&1
    # real	488m23.776s

    cat fb.galGal6.chainCheMyd1Link.txt
    # 538550235 bases of 1055588482 (51.019%) in intersection

    cat fb.galGal6.chainSynCheMyd1Link.txt
    # 439571636 bases of 1055588482 (41.642%) in intersection

    time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \
	galGal6 CheMyd1) > rbest.log 2>&1 &
    # real	356m1.191s

    cat fb.galGal6.chainRBest.CheMyd1.txt
    # 484498431 bases of 1055588482 (45.898%) in intersection

#############################################################################
# LASTZ chicken/galGal6 vs Houbara bustard/chlUnd1 - (DONE - 2018-10-18 - script/hiram)
    mkdir /hive/data/genomes/galGal6/bed/lastzChlUnd1.2018-10-18
    cd /hive/data/genomes/galGal6/bed/lastzChlUnd1.2018-10-18

   printf "# chicken vs Houbara bustard
# galGal6 vs chlUnd1
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.00/bin/lastz
BLASTZ_H=2000
BLASTZ_Y=3400
BLASTZ_L=4000
BLASTZ_K=2200
BLASTZ_M=254
BLASTZ_Q=/cluster/data/blastz/HoxD55.q

# TARGET: galGal6 - chicken - Gallus gallus
SEQ1_DIR=/hive/data/genomes/galGal6/galGal6.2bit
SEQ1_LEN=/hive/data/genomes/galGal6/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
SEQ1_LIMIT=40

# QUERY: chlUnd1 - Houbara bustard - Chlamydotis undulata macqueenii
SEQ2_DIR=/hive/data/genomes/chlUnd1/chlUnd1.2bit
SEQ2_LEN=/hive/data/genomes/chlUnd1/chrom.sizes
SEQ2_CHUNK=1000000
SEQ2_LIMIT=2000
SEQ2_LAP=0

BASE=/hive/data/genomes/galGal6/bed/lastzChlUnd1.2018-10-18
TMPDIR=/dev/shm
" > DEF

    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
      -workhorse=hgwdev -bigClusterHub=ku \
        -dbHost=hgwdev -smallClusterHub=ku \
          -fileServer=hgwdev -syntenicNet) > do.log 2>&1
    # real	444m5.490s

    cat fb.galGal6.chainChlUnd1Link.txt
    # 876572094 bases of 1055588482 (83.041%) in intersection

    cat fb.galGal6.chainSynChlUnd1Link.txt
    # 728906002 bases of 1055588482 (69.052%) in intersection

    time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \
	galGal6 ChlUnd1) > rbest.log 2>&1 &
    # real	315m54.274s

    cat fb.galGal6.chainRBest.ChlUnd1.txt
    # 792837683 bases of 1055588482 (75.109%) in intersection

#############################################################################
# LASTZ chicken/galGal6 vs Painted turtle/chrPic2 - (DONE - 2018-10-18 - script/hiram)
    mkdir /hive/data/genomes/galGal6/bed/lastzChrPic2.2018-10-18
    cd /hive/data/genomes/galGal6/bed/lastzChrPic2.2018-10-18

   printf "# chicken vs Painted turtle
# galGal6 vs chrPic2
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.00/bin/lastz
BLASTZ_H=2000
BLASTZ_Y=3400
BLASTZ_L=4000
BLASTZ_K=2200
BLASTZ_M=254
BLASTZ_Q=/cluster/data/blastz/HoxD55.q

# TARGET: galGal6 - chicken - Gallus gallus
SEQ1_DIR=/hive/data/genomes/galGal6/galGal6.2bit
SEQ1_LEN=/hive/data/genomes/galGal6/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
SEQ1_LIMIT=40

# QUERY: chrPic2 - Painted turtle - Chrysemys picta bellii
SEQ2_DIR=/hive/data/genomes/chrPic2/chrPic2.2bit
SEQ2_LEN=/hive/data/genomes/chrPic2/chrom.sizes
SEQ2_CHUNK=1000000
SEQ2_LIMIT=2000
SEQ2_LAP=0

BASE=/hive/data/genomes/galGal6/bed/lastzChrPic2.2018-10-18
TMPDIR=/dev/shm
" > DEF

    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
      -workhorse=hgwdev -bigClusterHub=ku \
        -dbHost=hgwdev -smallClusterHub=ku \
          -fileServer=hgwdev -syntenicNet) > do.log 2>&1
    # real	499m8.294s

    cat fb.galGal6.chainChrPic2Link.txt
    # 545995699 bases of 1055588482 (51.724%) in intersection

    cat fb.galGal6.chainSynChrPic2Link.txt
    # 441949079 bases of 1055588482 (41.868%) in intersection

    time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \
	galGal6 ChrPic2) > rbest.log 2>&1 &
    # real	392m57.089s

    cat fb.galGal6.chainRBest.ChrPic2.txt
    # 489464915 bases of 1055588482 (46.369%) in intersection

#############################################################################
# LASTZ chicken/galGal6 vs Rock pigeon/colLiv1 - (DONE - 2018-10-18 - script/hiram)
    mkdir /hive/data/genomes/galGal6/bed/lastzColLiv1.2018-10-18
    cd /hive/data/genomes/galGal6/bed/lastzColLiv1.2018-10-18

   printf "# chicken vs Rock pigeon
# galGal6 vs colLiv1
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.00/bin/lastz
BLASTZ_H=2000
BLASTZ_Y=3400
BLASTZ_L=4000
BLASTZ_K=2200
BLASTZ_M=254
BLASTZ_Q=/cluster/data/blastz/HoxD55.q

# TARGET: galGal6 - chicken - Gallus gallus
SEQ1_DIR=/hive/data/genomes/galGal6/galGal6.2bit
SEQ1_LEN=/hive/data/genomes/galGal6/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
SEQ1_LIMIT=40

# QUERY: colLiv1 - Rock pigeon - Columba livia
SEQ2_DIR=/hive/data/genomes/colLiv1/colLiv1.2bit
SEQ2_LEN=/hive/data/genomes/colLiv1/chrom.sizes
SEQ2_CHUNK=1000000
SEQ2_LIMIT=2000
SEQ2_LAP=0

BASE=/hive/data/genomes/galGal6/bed/lastzColLiv1.2018-10-18
TMPDIR=/dev/shm
" > DEF

    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
      -workhorse=hgwdev -bigClusterHub=ku \
        -dbHost=hgwdev -smallClusterHub=ku \
          -fileServer=hgwdev -syntenicNet) > do.log 2>&1
    # real	477m10.507s

    cat fb.galGal6.chainColLiv1Link.txt
    # 876908494 bases of 1055588482 (83.073%) in intersection

    cat fb.galGal6.chainSynColLiv1Link.txt
    # 766031947 bases of 1055588482 (72.569%) in intersection

    time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \
	galGal6 ColLiv1) > rbest.log 2>&1 &
    # real	314m13.764s

    cat fb.galGal6.chainRBest.ColLiv1.txt
    # 785036429 bases of 1055588482 (74.370%) in intersection

#############################################################################
# LASTZ chicken/galGal6 vs Speckled mousebird/colStr1 - (DONE - 2018-10-18 - script/hiram)
    mkdir /hive/data/genomes/galGal6/bed/lastzColStr1.2018-10-18
    cd /hive/data/genomes/galGal6/bed/lastzColStr1.2018-10-18

   printf "# chicken vs Speckled mousebird
# galGal6 vs colStr1
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.00/bin/lastz
BLASTZ_H=2000
BLASTZ_Y=3400
BLASTZ_L=4000
BLASTZ_K=2200
BLASTZ_M=254
BLASTZ_Q=/cluster/data/blastz/HoxD55.q

# TARGET: galGal6 - chicken - Gallus gallus
SEQ1_DIR=/hive/data/genomes/galGal6/galGal6.2bit
SEQ1_LEN=/hive/data/genomes/galGal6/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
SEQ1_LIMIT=40

# QUERY: colStr1 - Speckled mousebird - Colius striatus
SEQ2_DIR=/hive/data/genomes/colStr1/colStr1.2bit
SEQ2_LEN=/hive/data/genomes/colStr1/chrom.sizes
SEQ2_CHUNK=1000000
SEQ2_LIMIT=2000
SEQ2_LAP=0

BASE=/hive/data/genomes/galGal6/bed/lastzColStr1.2018-10-18
TMPDIR=/dev/shm
" > DEF

    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
      -workhorse=hgwdev -bigClusterHub=ku \
        -dbHost=hgwdev -smallClusterHub=ku \
          -fileServer=hgwdev -syntenicNet) > do.log 2>&1
    # real	587m56.997s

    cat fb.galGal6.chainColStr1Link.txt
    # 854884790 bases of 1055588482 (80.987%) in intersection

    cat fb.galGal6.chainSynColStr1Link.txt
    # 678861985 bases of 1055588482 (64.311%) in intersection

    time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \
	galGal6 ColStr1) > rbest.log 2>&1 &
    # real	441m29.228s

    cat fb.galGal6.chainRBest.ColStr1.txt
    # 760238251 bases of 1055588482 (72.020%) in intersection

#############################################################################
# LASTZ chicken/galGal6 vs American crow/corBra1 - (DONE - 2018-10-18 - script/hiram)
    mkdir /hive/data/genomes/galGal6/bed/lastzCorBra1.2018-10-18
    cd /hive/data/genomes/galGal6/bed/lastzCorBra1.2018-10-18

   printf "# chicken vs American crow
# galGal6 vs corBra1
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.00/bin/lastz
BLASTZ_H=2000
BLASTZ_Y=3400
BLASTZ_L=4000
BLASTZ_K=2200
BLASTZ_M=254
BLASTZ_Q=/cluster/data/blastz/HoxD55.q

# TARGET: galGal6 - chicken - Gallus gallus
SEQ1_DIR=/hive/data/genomes/galGal6/galGal6.2bit
SEQ1_LEN=/hive/data/genomes/galGal6/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
SEQ1_LIMIT=40

# QUERY: corBra1 - American crow - Corvus brachyrhynchos
SEQ2_DIR=/hive/data/genomes/corBra1/corBra1.2bit
SEQ2_LEN=/hive/data/genomes/corBra1/chrom.sizes
SEQ2_CHUNK=1000000
SEQ2_LIMIT=2000
SEQ2_LAP=0

BASE=/hive/data/genomes/galGal6/bed/lastzCorBra1.2018-10-18
TMPDIR=/dev/shm
" > DEF

    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
      -workhorse=hgwdev -bigClusterHub=ku \
        -dbHost=hgwdev -smallClusterHub=ku \
          -fileServer=hgwdev -syntenicNet) > do.log 2>&1
    # real	565m41.665s

    cat fb.galGal6.chainCorBra1Link.txt
    # 854798756 bases of 1055588482 (80.978%) in intersection

    cat fb.galGal6.chainSynCorBra1Link.txt
    # 732338012 bases of 1055588482 (69.377%) in intersection

    time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \
	galGal6 CorBra1) > rbest.log 2>&1 &
    # real	392m5.064s

    cat fb.galGal6.chainRBest.CorBra1.txt
    # 754104139 bases of 1055588482 (71.439%) in intersection

#############################################################################
# LASTZ chicken/galGal6 vs Hooded crow/corCor1 - (DONE - 2018-10-19 - script/hiram)
    mkdir /hive/data/genomes/galGal6/bed/lastzCorCor1.2018-10-19
    cd /hive/data/genomes/galGal6/bed/lastzCorCor1.2018-10-19

   printf "# chicken vs Hooded crow
# galGal6 vs corCor1
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.00/bin/lastz
BLASTZ_H=2000
BLASTZ_Y=3400
BLASTZ_L=4000
BLASTZ_K=2200
BLASTZ_M=254
BLASTZ_Q=/cluster/data/blastz/HoxD55.q

# TARGET: galGal6 - chicken - Gallus gallus
SEQ1_DIR=/hive/data/genomes/galGal6/galGal6.2bit
SEQ1_LEN=/hive/data/genomes/galGal6/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
SEQ1_LIMIT=40

# QUERY: corCor1 - Hooded crow - Corvus cornix cornix
SEQ2_DIR=/hive/data/genomes/corCor1/corCor1.2bit
SEQ2_LEN=/hive/data/genomes/corCor1/chrom.sizes
SEQ2_CHUNK=1000000
SEQ2_LIMIT=2000
SEQ2_LAP=0

BASE=/hive/data/genomes/galGal6/bed/lastzCorCor1.2018-10-19
TMPDIR=/dev/shm
" > DEF

    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
      -workhorse=hgwdev -bigClusterHub=ku \
        -dbHost=hgwdev -smallClusterHub=ku \
          -fileServer=hgwdev -syntenicNet) > do.log 2>&1
    # real	591m45.748s

    cat fb.galGal6.chainCorCor1Link.txt
    # 850530295 bases of 1055588482 (80.574%) in intersection

    cat fb.galGal6.chainSynCorCor1Link.txt
    # 718475664 bases of 1055588482 (68.064%) in intersection

    time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \
	galGal6 CorCor1) > rbest.log 2>&1 &
    # real	425m28.944s

    cat fb.galGal6.chainRBest.CorCor1.txt
    # 750021584 bases of 1055588482 (71.052%) in intersection

#############################################################################
# LASTZ chicken/galGal6 vs Japanese quail/cotJap1 - (DONE - 2018-10-19 - script/hiram)
    mkdir /hive/data/genomes/galGal6/bed/lastzCotJap1.2018-10-19
    cd /hive/data/genomes/galGal6/bed/lastzCotJap1.2018-10-19

   printf "# chicken vs Japanese quail
# galGal6 vs cotJap1
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.00/bin/lastz
BLASTZ_H=2000
BLASTZ_Y=3400
BLASTZ_L=4000
BLASTZ_K=2200
BLASTZ_M=254
BLASTZ_Q=/cluster/data/blastz/HoxD55.q

# TARGET: galGal6 - chicken - Gallus gallus
SEQ1_DIR=/hive/data/genomes/galGal6/galGal6.2bit
SEQ1_LEN=/hive/data/genomes/galGal6/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
SEQ1_LIMIT=40

# QUERY: cotJap1 - Japanese quail - Coturnix japonica
SEQ2_DIR=/hive/data/genomes/cotJap1/cotJap1.2bit
SEQ2_LEN=/hive/data/genomes/cotJap1/chrom.sizes
SEQ2_CHUNK=1000000
SEQ2_LIMIT=2000
SEQ2_LAP=0

BASE=/hive/data/genomes/galGal6/bed/lastzCotJap1.2018-10-19
TMPDIR=/dev/shm
" > DEF

    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
      -workhorse=hgwdev -bigClusterHub=ku \
        -dbHost=hgwdev -smallClusterHub=ku \
          -fileServer=hgwdev -syntenicNet) > do.log 2>&1
    # real	402m14.191s

    cat fb.galGal6.chainCotJap1Link.txt
    # 592408208 bases of 1055588482 (56.121%) in intersection

    cat fb.galGal6.chainSynCotJap1Link.txt
    # 428571708 bases of 1055588482 (40.600%) in intersection

    time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \
	galGal6 CotJap1) > rbest.log 2>&1 &
    # real	331m41.351s

    cat fb.galGal6.chainRBest.CotJap1.txt
    # 431816963 bases of 1055588482 (40.908%) in intersection

#############################################################################
# LASTZ chicken/galGal6 vs Common cuckoo/cucCan1 - (DONE - 2018-10-19 - script/hiram)
    mkdir /hive/data/genomes/galGal6/bed/lastzCucCan1.2018-10-19
    cd /hive/data/genomes/galGal6/bed/lastzCucCan1.2018-10-19

   printf "# chicken vs Common cuckoo
# galGal6 vs cucCan1
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.00/bin/lastz
BLASTZ_H=2000
BLASTZ_Y=3400
BLASTZ_L=4000
BLASTZ_K=2200
BLASTZ_M=254
BLASTZ_Q=/cluster/data/blastz/HoxD55.q

# TARGET: galGal6 - chicken - Gallus gallus
SEQ1_DIR=/hive/data/genomes/galGal6/galGal6.2bit
SEQ1_LEN=/hive/data/genomes/galGal6/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
SEQ1_LIMIT=40

# QUERY: cucCan1 - Common cuckoo - Cuculus canorus
SEQ2_DIR=/hive/data/genomes/cucCan1/cucCan1.2bit
SEQ2_LEN=/hive/data/genomes/cucCan1/chrom.sizes
SEQ2_CHUNK=1000000
SEQ2_LIMIT=2000
SEQ2_LAP=0

BASE=/hive/data/genomes/galGal6/bed/lastzCucCan1.2018-10-19
TMPDIR=/dev/shm
" > DEF

    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
      -workhorse=hgwdev -bigClusterHub=ku \
        -dbHost=hgwdev -smallClusterHub=ku \
          -fileServer=hgwdev -syntenicNet) > do.log 2>&1
    # real	495m53.604s

    cat fb.galGal6.chainCucCan1Link.txt
    # 877724050 bases of 1055588482 (83.150%) in intersection

    cat fb.galGal6.chainSynCucCan1Link.txt
    # 761013196 bases of 1055588482 (72.094%) in intersection

    time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \
	galGal6 CucCan1) > rbest.log 2>&1 &
    # real	330m35.696s

    cat fb.galGal6.chainRBest.CucCan1.txt
    # 784860736 bases of 1055588482 (74.353%) in intersection

#############################################################################
# LASTZ chicken/galGal6 vs Little egret/egrGar1 - (DONE - 2018-10-19 - script/hiram)
    mkdir /hive/data/genomes/galGal6/bed/lastzEgrGar1.2018-10-19
    cd /hive/data/genomes/galGal6/bed/lastzEgrGar1.2018-10-19

   printf "# chicken vs Little egret
# galGal6 vs egrGar1
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.00/bin/lastz
BLASTZ_H=2000
BLASTZ_Y=3400
BLASTZ_L=4000
BLASTZ_K=2200
BLASTZ_M=254
BLASTZ_Q=/cluster/data/blastz/HoxD55.q

# TARGET: galGal6 - chicken - Gallus gallus
SEQ1_DIR=/hive/data/genomes/galGal6/galGal6.2bit
SEQ1_LEN=/hive/data/genomes/galGal6/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
SEQ1_LIMIT=40

# QUERY: egrGar1 - Little egret - Egretta garzetta
SEQ2_DIR=/hive/data/genomes/egrGar1/egrGar1.2bit
SEQ2_LEN=/hive/data/genomes/egrGar1/chrom.sizes
SEQ2_CHUNK=1000000
SEQ2_LIMIT=2000
SEQ2_LAP=0

BASE=/hive/data/genomes/galGal6/bed/lastzEgrGar1.2018-10-19
TMPDIR=/dev/shm
" > DEF

    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
      -workhorse=hgwdev -bigClusterHub=ku \
        -dbHost=hgwdev -smallClusterHub=ku \
          -fileServer=hgwdev -syntenicNet) > do.log 2>&1
    # real	380m24.844s

    cat fb.galGal6.chainEgrGar1Link.txt
    # 903470826 bases of 1055588482 (85.589%) in intersection

    cat fb.galGal6.chainSynEgrGar1Link.txt
    # 807513965 bases of 1055588482 (76.499%) in intersection

    time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \
	galGal6 EgrGar1) > rbest.log 2>&1 &
    # real	242m14.176s

    cat fb.galGal6.chainRBest.EgrGar1.txt
    # 823806797 bases of 1055588482 (78.042%) in intersection

#############################################################################
# LASTZ chicken/galGal6 vs Sunbittern/eurHel1 - (DONE - 2018-10-19 - script/hiram)
    mkdir /hive/data/genomes/galGal6/bed/lastzEurHel1.2018-10-19
    cd /hive/data/genomes/galGal6/bed/lastzEurHel1.2018-10-19

   printf "# chicken vs Sunbittern
# galGal6 vs eurHel1
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.00/bin/lastz
BLASTZ_H=2000
BLASTZ_Y=3400
BLASTZ_L=4000
BLASTZ_K=2200
BLASTZ_M=254
BLASTZ_Q=/cluster/data/blastz/HoxD55.q

# TARGET: galGal6 - chicken - Gallus gallus
SEQ1_DIR=/hive/data/genomes/galGal6/galGal6.2bit
SEQ1_LEN=/hive/data/genomes/galGal6/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
SEQ1_LIMIT=40

# QUERY: eurHel1 - Sunbittern - Eurypyga helias
SEQ2_DIR=/hive/data/genomes/eurHel1/eurHel1.2bit
SEQ2_LEN=/hive/data/genomes/eurHel1/chrom.sizes
SEQ2_CHUNK=1000000
SEQ2_LIMIT=2000
SEQ2_LAP=0

BASE=/hive/data/genomes/galGal6/bed/lastzEurHel1.2018-10-19
TMPDIR=/dev/shm
" > DEF

    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
      -workhorse=hgwdev -bigClusterHub=ku \
        -dbHost=hgwdev -smallClusterHub=ku \
          -fileServer=hgwdev -syntenicNet) > do.log 2>&1
    # real	691m55.179s

    cat fb.galGal6.chainEurHel1Link.txt
    # 870082807 bases of 1055588482 (82.426%) in intersection

    cat fb.galGal6.chainSynEurHel1Link.txt
    # 714159632 bases of 1055588482 (67.655%) in intersection

    time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \
	galGal6 EurHel1) > rbest.log 2>&1 &
    # real	387m45.136s

    cat fb.galGal6.chainRBest.EurHel1.txt
    # 783796534 bases of 1055588482 (74.252%) in intersection

#############################################################################
# LASTZ chicken/galGal6 vs Saker falcon/falChe1 - (DONE - 2018-10-19 - script/hiram)
    mkdir /hive/data/genomes/galGal6/bed/lastzFalChe1.2018-10-19
    cd /hive/data/genomes/galGal6/bed/lastzFalChe1.2018-10-19

   printf "# chicken vs Saker falcon
# galGal6 vs falChe1
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.00/bin/lastz
BLASTZ_H=2000
BLASTZ_Y=3400
BLASTZ_L=4000
BLASTZ_K=2200
BLASTZ_M=254
BLASTZ_Q=/cluster/data/blastz/HoxD55.q

# TARGET: galGal6 - chicken - Gallus gallus
SEQ1_DIR=/hive/data/genomes/galGal6/galGal6.2bit
SEQ1_LEN=/hive/data/genomes/galGal6/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
SEQ1_LIMIT=40

# QUERY: falChe1 - Saker falcon - Falco cherrug
SEQ2_DIR=/hive/data/genomes/falChe1/falChe1.2bit
SEQ2_LEN=/hive/data/genomes/falChe1/chrom.sizes
SEQ2_CHUNK=1000000
SEQ2_LIMIT=2000
SEQ2_LAP=0

BASE=/hive/data/genomes/galGal6/bed/lastzFalChe1.2018-10-19
TMPDIR=/dev/shm
" > DEF

    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
      -workhorse=hgwdev -bigClusterHub=ku \
        -dbHost=hgwdev -smallClusterHub=ku \
          -fileServer=hgwdev -syntenicNet) > do.log 2>&1
    # real	624m12.224s

    cat fb.galGal6.chainFalChe1Link.txt
    # 911415065 bases of 1055588482 (86.342%) in intersection

    cat fb.galGal6.chainSynFalChe1Link.txt
    # 807507886 bases of 1055588482 (76.498%) in intersection

    time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \
	galGal6 FalChe1) > rbest.log 2>&1 &
    # real	273m9.858s

    cat fb.galGal6.chainRBest.FalChe1.txt
    # 828810487 bases of 1055588482 (78.516%) in intersection

#############################################################################
# LASTZ chicken/galGal6 vs Peregrine falcon/falPer1 - (DONE - 2018-10-19 - script/hiram)
    mkdir /hive/data/genomes/galGal6/bed/lastzFalPer1.2018-10-19
    cd /hive/data/genomes/galGal6/bed/lastzFalPer1.2018-10-19

   printf "# chicken vs Peregrine falcon
# galGal6 vs falPer1
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.00/bin/lastz
BLASTZ_H=2000
BLASTZ_Y=3400
BLASTZ_L=4000
BLASTZ_K=2200
BLASTZ_M=254
BLASTZ_Q=/cluster/data/blastz/HoxD55.q

# TARGET: galGal6 - chicken - Gallus gallus
SEQ1_DIR=/hive/data/genomes/galGal6/galGal6.2bit
SEQ1_LEN=/hive/data/genomes/galGal6/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
SEQ1_LIMIT=40

# QUERY: falPer1 - Peregrine falcon - Falco peregrinus
SEQ2_DIR=/hive/data/genomes/falPer1/falPer1.2bit
SEQ2_LEN=/hive/data/genomes/falPer1/chrom.sizes
SEQ2_CHUNK=1000000
SEQ2_LIMIT=2000
SEQ2_LAP=0

BASE=/hive/data/genomes/galGal6/bed/lastzFalPer1.2018-10-19
TMPDIR=/dev/shm
" > DEF

    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
      -workhorse=hgwdev -bigClusterHub=ku \
        -dbHost=hgwdev -smallClusterHub=ku \
          -fileServer=hgwdev -syntenicNet) > do.log 2>&1
    # real	625m24.573s

    cat fb.galGal6.chainFalPer1Link.txt
    # 913080823 bases of 1055588482 (86.500%) in intersection

    cat fb.galGal6.chainSynFalPer1Link.txt
    # 812447015 bases of 1055588482 (76.966%) in intersection

    time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \
	galGal6 FalPer1) > rbest.log 2>&1 &
    # real	274m12.882s

    cat fb.galGal6.chainRBest.FalPer1.txt
    # 830510373 bases of 1055588482 (78.677%) in intersection

#############################################################################
# LASTZ chicken/galGal6 vs Northern fulmar/fulGla1 - (DONE - 2018-10-19 - script/hiram)
    mkdir /hive/data/genomes/galGal6/bed/lastzFulGla1.2018-10-19
    cd /hive/data/genomes/galGal6/bed/lastzFulGla1.2018-10-19

   printf "# chicken vs Northern fulmar
# galGal6 vs fulGla1
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.00/bin/lastz
BLASTZ_H=2000
BLASTZ_Y=3400
BLASTZ_L=4000
BLASTZ_K=2200
BLASTZ_M=254
BLASTZ_Q=/cluster/data/blastz/HoxD55.q

# TARGET: galGal6 - chicken - Gallus gallus
SEQ1_DIR=/hive/data/genomes/galGal6/galGal6.2bit
SEQ1_LEN=/hive/data/genomes/galGal6/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
SEQ1_LIMIT=40

# QUERY: fulGla1 - Northern fulmar - Fulmarus glacialis
SEQ2_DIR=/hive/data/genomes/fulGla1/fulGla1.2bit
SEQ2_LEN=/hive/data/genomes/fulGla1/chrom.sizes
SEQ2_CHUNK=1000000
SEQ2_LIMIT=2000
SEQ2_LAP=0

BASE=/hive/data/genomes/galGal6/bed/lastzFulGla1.2018-10-19
TMPDIR=/dev/shm
" > DEF

    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
      -workhorse=hgwdev -bigClusterHub=ku \
        -dbHost=hgwdev -smallClusterHub=ku \
          -fileServer=hgwdev -syntenicNet) > do.log 2>&1
    # real	599m13.056s

    cat fb.galGal6.chainFulGla1Link.txt
    # 900756652 bases of 1055588482 (85.332%) in intersection

    cat fb.galGal6.chainSynFulGla1Link.txt
    # 771539763 bases of 1055588482 (73.091%) in intersection

    time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \
	galGal6 FulGla1) > rbest.log 2>&1 &
    # real	300m46.949s

    cat fb.galGal6.chainRBest.FulGla1.txt
    # 824502605 bases of 1055588482 (78.108%) in intersection

#############################################################################
# LASTZ chicken/galGal6 vs Red-throated loon/gavSte1 - (DONE - 2018-10-19 - script/hiram)
    mkdir /hive/data/genomes/galGal6/bed/lastzGavSte1.2018-10-19
    cd /hive/data/genomes/galGal6/bed/lastzGavSte1.2018-10-19

   printf "# chicken vs Red-throated loon
# galGal6 vs gavSte1
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.00/bin/lastz
BLASTZ_H=2000
BLASTZ_Y=3400
BLASTZ_L=4000
BLASTZ_K=2200
BLASTZ_M=254
BLASTZ_Q=/cluster/data/blastz/HoxD55.q

# TARGET: galGal6 - chicken - Gallus gallus
SEQ1_DIR=/hive/data/genomes/galGal6/galGal6.2bit
SEQ1_LEN=/hive/data/genomes/galGal6/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
SEQ1_LIMIT=40

# QUERY: gavSte1 - Red-throated loon - Gavia stellata
SEQ2_DIR=/hive/data/genomes/gavSte1/gavSte1.2bit
SEQ2_LEN=/hive/data/genomes/gavSte1/chrom.sizes
SEQ2_CHUNK=1000000
SEQ2_LIMIT=2000
SEQ2_LAP=0

BASE=/hive/data/genomes/galGal6/bed/lastzGavSte1.2018-10-19
TMPDIR=/dev/shm
" > DEF

    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
      -workhorse=hgwdev -bigClusterHub=ku \
        -dbHost=hgwdev -smallClusterHub=ku \
          -fileServer=hgwdev -syntenicNet) > do.log 2>&1
    # real	612m10.148s

    cat fb.galGal6.chainGavSte1Link.txt
    # 894263882 bases of 1055588482 (84.717%) in intersection

    cat fb.galGal6.chainSynGavSte1Link.txt
    # 761960610 bases of 1055588482 (72.183%) in intersection

    time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \
	galGal6 GavSte1) > rbest.log 2>&1 &
    # real	314m22.814s

    cat fb.galGal6.chainRBest.GavSte1.txt
    # 818435214 bases of 1055588482 (77.534%) in intersection

#############################################################################
# LASTZ chicken/galGal6 vs Medium ground finch/geoFor1 - (DONE - 2018-10-19 - script/hiram)
    mkdir /hive/data/genomes/galGal6/bed/lastzGeoFor1.2018-10-19
    cd /hive/data/genomes/galGal6/bed/lastzGeoFor1.2018-10-19

   printf "# chicken vs Medium ground finch
# galGal6 vs geoFor1
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.00/bin/lastz
BLASTZ_H=2000
BLASTZ_Y=3400
BLASTZ_L=4000
BLASTZ_K=2200
BLASTZ_M=254
BLASTZ_Q=/cluster/data/blastz/HoxD55.q

# TARGET: galGal6 - chicken - Gallus gallus
SEQ1_DIR=/hive/data/genomes/galGal6/galGal6.2bit
SEQ1_LEN=/hive/data/genomes/galGal6/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
SEQ1_LIMIT=40

# QUERY: geoFor1 - Medium ground finch - Geospiza fortis
SEQ2_DIR=/hive/data/genomes/geoFor1/geoFor1.2bit
SEQ2_LEN=/hive/data/genomes/geoFor1/chrom.sizes
SEQ2_CHUNK=1000000
SEQ2_LIMIT=2000
SEQ2_LAP=0

BASE=/hive/data/genomes/galGal6/bed/lastzGeoFor1.2018-10-19
TMPDIR=/dev/shm
" > DEF

    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
      -workhorse=hgwdev -bigClusterHub=ku \
        -dbHost=hgwdev -smallClusterHub=ku \
          -fileServer=hgwdev -syntenicNet) > do.log 2>&1
    # real	765m20.987s

    cat fb.galGal6.chainGeoFor1Link.txt
    # 837073388 bases of 1055588482 (79.299%) in intersection

    cat fb.galGal6.chainSynGeoFor1Link.txt
    # 706945549 bases of 1055588482 (66.972%) in intersection

    time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \
	galGal6 GeoFor1) > rbest.log 2>&1 &
    # real	423m23.442s

    cat fb.galGal6.chainRBest.GeoFor1.txt
    # 731219352 bases of 1055588482 (69.271%) in intersection

#############################################################################
# LASTZ chicken/galGal6 vs White-tailed eagle/halAlb1 - (DONE - 2018-10-20 - script/hiram)
    mkdir /hive/data/genomes/galGal6/bed/lastzHalAlb1.2018-10-20
    cd /hive/data/genomes/galGal6/bed/lastzHalAlb1.2018-10-20

   printf "# chicken vs White-tailed eagle
# galGal6 vs halAlb1
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.00/bin/lastz
BLASTZ_H=2000
BLASTZ_Y=3400
BLASTZ_L=4000
BLASTZ_K=2200
BLASTZ_M=254
BLASTZ_Q=/cluster/data/blastz/HoxD55.q

# TARGET: galGal6 - chicken - Gallus gallus
SEQ1_DIR=/hive/data/genomes/galGal6/galGal6.2bit
SEQ1_LEN=/hive/data/genomes/galGal6/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
SEQ1_LIMIT=40

# QUERY: halAlb1 - White-tailed eagle - Haliaeetus albicilla
SEQ2_DIR=/hive/data/genomes/halAlb1/halAlb1.2bit
SEQ2_LEN=/hive/data/genomes/halAlb1/chrom.sizes
SEQ2_CHUNK=1000000
SEQ2_LIMIT=2000
SEQ2_LAP=0

BASE=/hive/data/genomes/galGal6/bed/lastzHalAlb1.2018-10-20
TMPDIR=/dev/shm
" > DEF

    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
      -workhorse=hgwdev -bigClusterHub=ku \
        -dbHost=hgwdev -smallClusterHub=ku \
          -fileServer=hgwdev -syntenicNet) > do.log 2>&1
    # real	425m10.485s

    cat fb.galGal6.chainHalAlb1Link.txt
    # 897213301 bases of 1055588482 (84.997%) in intersection

    cat fb.galGal6.chainSynHalAlb1Link.txt
    # 772402407 bases of 1055588482 (73.173%) in intersection

    time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \
	galGal6 HalAlb1) > rbest.log 2>&1 &
    # real	299m24.177s

    cat fb.galGal6.chainRBest.HalAlb1.txt
    # 819350653 bases of 1055588482 (77.620%) in intersection

#############################################################################
# LASTZ chicken/galGal6 vs Bald eagle/halLeu1 - (DONE - 2018-10-20 - script/hiram)
    mkdir /hive/data/genomes/galGal6/bed/lastzHalLeu1.2018-10-20
    cd /hive/data/genomes/galGal6/bed/lastzHalLeu1.2018-10-20

   printf "# chicken vs Bald eagle
# galGal6 vs halLeu1
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.00/bin/lastz
BLASTZ_H=2000
BLASTZ_Y=3400
BLASTZ_L=4000
BLASTZ_K=2200
BLASTZ_M=254
BLASTZ_Q=/cluster/data/blastz/HoxD55.q

# TARGET: galGal6 - chicken - Gallus gallus
SEQ1_DIR=/hive/data/genomes/galGal6/galGal6.2bit
SEQ1_LEN=/hive/data/genomes/galGal6/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
SEQ1_LIMIT=40

# QUERY: halLeu1 - Bald eagle - Haliaeetus leucocephalus
SEQ2_DIR=/hive/data/genomes/halLeu1/halLeu1.2bit
SEQ2_LEN=/hive/data/genomes/halLeu1/chrom.sizes
SEQ2_CHUNK=1000000
SEQ2_LIMIT=2000
SEQ2_LAP=0

BASE=/hive/data/genomes/galGal6/bed/lastzHalLeu1.2018-10-20
TMPDIR=/dev/shm
" > DEF

    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
      -workhorse=hgwdev -bigClusterHub=ku \
        -dbHost=hgwdev -smallClusterHub=ku \
          -fileServer=hgwdev -syntenicNet) > do.log 2>&1
    # real	384m24.469s

    cat fb.galGal6.chainHalLeu1Link.txt
    # 917551459 bases of 1055588482 (86.923%) in intersection

    cat fb.galGal6.chainSynHalLeu1Link.txt
    # 820998974 bases of 1055588482 (77.776%) in intersection

    time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \
	galGal6 HalLeu1) > rbest.log 2>&1 &
    # real	247m10.238s

    cat fb.galGal6.chainRBest.HalLeu1.txt
    # 838255932 bases of 1055588482 (79.411%) in intersection

#############################################################################
# LASTZ chicken/galGal6 vs Cuckoo roller/lepDis1 - (DONE - 2018-10-20 - script/hiram)
    mkdir /hive/data/genomes/galGal6/bed/lastzLepDis1.2018-10-20
    cd /hive/data/genomes/galGal6/bed/lastzLepDis1.2018-10-20

   printf "# chicken vs Cuckoo roller
# galGal6 vs lepDis1
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.00/bin/lastz
BLASTZ_H=2000
BLASTZ_Y=3400
BLASTZ_L=4000
BLASTZ_K=2200
BLASTZ_M=254
BLASTZ_Q=/cluster/data/blastz/HoxD55.q

# TARGET: galGal6 - chicken - Gallus gallus
SEQ1_DIR=/hive/data/genomes/galGal6/galGal6.2bit
SEQ1_LEN=/hive/data/genomes/galGal6/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
SEQ1_LIMIT=40

# QUERY: lepDis1 - Cuckoo roller - Leptosomus discolor
SEQ2_DIR=/hive/data/genomes/lepDis1/lepDis1.2bit
SEQ2_LEN=/hive/data/genomes/lepDis1/chrom.sizes
SEQ2_CHUNK=1000000
SEQ2_LIMIT=2000
SEQ2_LAP=0

BASE=/hive/data/genomes/galGal6/bed/lastzLepDis1.2018-10-20
TMPDIR=/dev/shm
" > DEF

    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
      -workhorse=hgwdev -bigClusterHub=ku \
        -dbHost=hgwdev -smallClusterHub=ku \
          -fileServer=hgwdev -syntenicNet) > do.log 2>&1
    # real	483m47.811s

    cat fb.galGal6.chainLepDis1Link.txt
    # 897470746 bases of 1055588482 (85.021%) in intersection

    cat fb.galGal6.chainSynLepDis1Link.txt
    # 763954799 bases of 1055588482 (72.372%) in intersection

    time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \
	galGal6 LepDis1) > rbest.log 2>&1 &
    # real	346m34.314s

    cat fb.galGal6.chainRBest.LepDis1.txt
    # 818033338 bases of 1055588482 (77.495%) in intersection

#############################################################################
# LASTZ chicken/galGal6 vs Arctic lamprey/letCam1 - (DONE - 2018-10-20 - script/hiram)
    mkdir /hive/data/genomes/galGal6/bed/lastzLetCam1.2018-10-20
    cd /hive/data/genomes/galGal6/bed/lastzLetCam1.2018-10-20

   printf "# chicken vs Arctic lamprey
# galGal6 vs letCam1
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.00/bin/lastz
BLASTZ_H=2000
BLASTZ_Y=3400
BLASTZ_L=4000
BLASTZ_K=2200
BLASTZ_M=254
BLASTZ_Q=/cluster/data/blastz/HoxD55.q

# TARGET: galGal6 - chicken - Gallus gallus
SEQ1_DIR=/hive/data/genomes/galGal6/galGal6.2bit
SEQ1_LEN=/hive/data/genomes/galGal6/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
SEQ1_LIMIT=40

# QUERY: letCam1 - Arctic lamprey - Lethenteron camtschaticum
SEQ2_DIR=/hive/data/genomes/letCam1/letCam1.2bit
SEQ2_LEN=/hive/data/genomes/letCam1/chrom.sizes
SEQ2_CHUNK=1000000
SEQ2_LIMIT=2000
SEQ2_LAP=0

BASE=/hive/data/genomes/galGal6/bed/lastzLetCam1.2018-10-20
TMPDIR=/dev/shm
" > DEF

    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
      -workhorse=hgwdev -bigClusterHub=ku \
        -dbHost=hgwdev -smallClusterHub=ku \
          -fileServer=hgwdev -syntenicNet) > do.log 2>&1
    # real	87m59.672s

    cat fb.galGal6.chainLetCam1Link.txt
    # 35206160 bases of 1055588482 (3.335%) in intersection

    cat fb.galGal6.chainSynLetCam1Link.txt
    # 1547533 bases of 1055588482 (0.147%) in intersection

    time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \
	galGal6 LetCam1) > rbest.log 2>&1 &
    # real	57m29.804s

    cat fb.galGal6.chainRBest.LetCam1.txt
    # 23080040 bases of 1055588482 (2.186%) in intersection

#############################################################################
# LASTZ chicken/galGal6 vs Zebra mbuna/mayZeb1 - (DONE - 2018-10-20 - script/hiram)
    mkdir /hive/data/genomes/galGal6/bed/lastzMayZeb1.2018-10-20
    cd /hive/data/genomes/galGal6/bed/lastzMayZeb1.2018-10-20

   printf "# chicken vs Zebra mbuna
# galGal6 vs mayZeb1
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.00/bin/lastz
BLASTZ_H=2000
BLASTZ_Y=3400
BLASTZ_L=4000
BLASTZ_K=2200
BLASTZ_M=254
BLASTZ_Q=/cluster/data/blastz/HoxD55.q

# TARGET: galGal6 - chicken - Gallus gallus
SEQ1_DIR=/hive/data/genomes/galGal6/galGal6.2bit
SEQ1_LEN=/hive/data/genomes/galGal6/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
SEQ1_LIMIT=40

# QUERY: mayZeb1 - Zebra mbuna - Maylandia zebra
SEQ2_DIR=/hive/data/genomes/mayZeb1/mayZeb1.2bit
SEQ2_LEN=/hive/data/genomes/mayZeb1/chrom.sizes
SEQ2_CHUNK=1000000
SEQ2_LIMIT=2000
SEQ2_LAP=0

BASE=/hive/data/genomes/galGal6/bed/lastzMayZeb1.2018-10-20
TMPDIR=/dev/shm
" > DEF

    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
      -workhorse=hgwdev -bigClusterHub=ku \
        -dbHost=hgwdev -smallClusterHub=ku \
          -fileServer=hgwdev -syntenicNet) > do.log 2>&1
    # real	95m40.688s

    cat fb.galGal6.chainMayZeb1Link.txt
    # 47913341 bases of 1055588482 (4.539%) in intersection

    cat fb.galGal6.chainSynMayZeb1Link.txt
    # 14297083 bases of 1055588482 (1.354%) in intersection

    time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \
	galGal6 MayZeb1) > rbest.log 2>&1 &
    # real	67m51.802s

    cat fb.galGal6.chainRBest.MayZeb1.txt
    # 39264653 bases of 1055588482 (3.720%) in intersection

#############################################################################
# LASTZ chicken/galGal6 vs Budgerigar/melUnd1 - (DONE - 2018-10-20 - script/hiram)
    mkdir /hive/data/genomes/galGal6/bed/lastzMelUnd1.2018-10-20
    cd /hive/data/genomes/galGal6/bed/lastzMelUnd1.2018-10-20

   printf "# chicken vs Budgerigar
# galGal6 vs melUnd1
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.00/bin/lastz
BLASTZ_H=2000
BLASTZ_Y=3400
BLASTZ_L=4000
BLASTZ_K=2200
BLASTZ_M=254
BLASTZ_Q=/cluster/data/blastz/HoxD55.q

# TARGET: galGal6 - chicken - Gallus gallus
SEQ1_DIR=/hive/data/genomes/galGal6/galGal6.2bit
SEQ1_LEN=/hive/data/genomes/galGal6/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
SEQ1_LIMIT=40

# QUERY: melUnd1 - Budgerigar - Melopsittacus undulatus
SEQ2_DIR=/hive/data/genomes/melUnd1/melUnd1.2bit
SEQ2_LEN=/hive/data/genomes/melUnd1/chrom.sizes
SEQ2_CHUNK=1000000
SEQ2_LIMIT=2000
SEQ2_LAP=0

BASE=/hive/data/genomes/galGal6/bed/lastzMelUnd1.2018-10-20
TMPDIR=/dev/shm
" > DEF

    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
      -workhorse=hgwdev -bigClusterHub=ku \
        -dbHost=hgwdev -smallClusterHub=ku \
          -fileServer=hgwdev -syntenicNet) > do.log 2>&1
    # real	578m59.698s

    cat fb.galGal6.chainMelUnd1Link.txt
    # 862351682 bases of 1055588482 (81.694%) in intersection

    cat fb.galGal6.chainSynMelUnd1Link.txt
    # 737018487 bases of 1055588482 (69.821%) in intersection

    time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \
	galGal6 MelUnd1) > rbest.log 2>&1 &
    # real	424m30.658s

    cat fb.galGal6.chainRBest.MelUnd1.txt
    # 765760426 bases of 1055588482 (72.543%) in intersection

#############################################################################
# LASTZ chicken/galGal6 vs Northern carmine bee-eater/merNub1 - (DONE - 2018-10-20 - script/hiram)
    mkdir /hive/data/genomes/galGal6/bed/lastzMerNub1.2018-10-20
    cd /hive/data/genomes/galGal6/bed/lastzMerNub1.2018-10-20

   printf "# chicken vs Northern carmine bee-eater
# galGal6 vs merNub1
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.00/bin/lastz
BLASTZ_H=2000
BLASTZ_Y=3400
BLASTZ_L=4000
BLASTZ_K=2200
BLASTZ_M=254
BLASTZ_Q=/cluster/data/blastz/HoxD55.q

# TARGET: galGal6 - chicken - Gallus gallus
SEQ1_DIR=/hive/data/genomes/galGal6/galGal6.2bit
SEQ1_LEN=/hive/data/genomes/galGal6/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
SEQ1_LIMIT=40

# QUERY: merNub1 - Northern carmine bee-eater - Merops nubicus
SEQ2_DIR=/hive/data/genomes/merNub1/merNub1.2bit
SEQ2_LEN=/hive/data/genomes/merNub1/chrom.sizes
SEQ2_CHUNK=1000000
SEQ2_LIMIT=2000
SEQ2_LAP=0

BASE=/hive/data/genomes/galGal6/bed/lastzMerNub1.2018-10-20
TMPDIR=/dev/shm
" > DEF

    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
      -workhorse=hgwdev -bigClusterHub=ku \
        -dbHost=hgwdev -smallClusterHub=ku \
          -fileServer=hgwdev -syntenicNet) > do.log 2>&1
    # real	609m53.704s

    cat fb.galGal6.chainMerNub1Link.txt
    # 855219539 bases of 1055588482 (81.018%) in intersection

    cat fb.galGal6.chainSynMerNub1Link.txt
    # 689682468 bases of 1055588482 (65.336%) in intersection

    time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \
	galGal6 MerNub1) > rbest.log 2>&1 &
    # real	461m12.202s

    cat fb.galGal6.chainRBest.MerNub1.txt
    # 762543217 bases of 1055588482 (72.239%) in intersection

#############################################################################
# LASTZ chicken/galGal6 vs Brown roatelo/mesUni1 - (DONE - 2018-10-20 - script/hiram)
    mkdir /hive/data/genomes/galGal6/bed/lastzMesUni1.2018-10-20
    cd /hive/data/genomes/galGal6/bed/lastzMesUni1.2018-10-20

   printf "# chicken vs Brown roatelo
# galGal6 vs mesUni1
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.00/bin/lastz
BLASTZ_H=2000
BLASTZ_Y=3400
BLASTZ_L=4000
BLASTZ_K=2200
BLASTZ_M=254
BLASTZ_Q=/cluster/data/blastz/HoxD55.q

# TARGET: galGal6 - chicken - Gallus gallus
SEQ1_DIR=/hive/data/genomes/galGal6/galGal6.2bit
SEQ1_LEN=/hive/data/genomes/galGal6/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
SEQ1_LIMIT=40

# QUERY: mesUni1 - Brown roatelo - Mesitornis unicolor
SEQ2_DIR=/hive/data/genomes/mesUni1/mesUni1.2bit
SEQ2_LEN=/hive/data/genomes/mesUni1/chrom.sizes
SEQ2_CHUNK=1000000
SEQ2_LIMIT=2000
SEQ2_LAP=0

BASE=/hive/data/genomes/galGal6/bed/lastzMesUni1.2018-10-20
TMPDIR=/dev/shm
" > DEF

    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
      -workhorse=hgwdev -bigClusterHub=ku \
        -dbHost=hgwdev -smallClusterHub=ku \
          -fileServer=hgwdev -syntenicNet) > do.log 2>&1
    # real	515m50.332s

    cat fb.galGal6.chainMesUni1Link.txt
    # 872437783 bases of 1055588482 (82.649%) in intersection

    cat fb.galGal6.chainSynMesUni1Link.txt
    # 712722916 bases of 1055588482 (67.519%) in intersection

    time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \
	galGal6 MesUni1) > rbest.log 2>&1 &
    # real	382m17.567s

    cat fb.galGal6.chainRBest.MesUni1.txt
    # 780887325 bases of 1055588482 (73.976%) in intersection

#############################################################################
# LASTZ chicken/galGal6 vs Tibetan frog/nanPar1 - (DONE - 2018-10-20 - script/hiram)
    mkdir /hive/data/genomes/galGal6/bed/lastzNanPar1.2018-10-20
    cd /hive/data/genomes/galGal6/bed/lastzNanPar1.2018-10-20

   printf "# chicken vs Tibetan frog
# galGal6 vs nanPar1
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.00/bin/lastz
BLASTZ_H=2000
BLASTZ_Y=3400
BLASTZ_L=4000
BLASTZ_K=2200
BLASTZ_M=254
BLASTZ_Q=/cluster/data/blastz/HoxD55.q

# TARGET: galGal6 - chicken - Gallus gallus
SEQ1_DIR=/hive/data/genomes/galGal6/galGal6.2bit
SEQ1_LEN=/hive/data/genomes/galGal6/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
SEQ1_LIMIT=40

# QUERY: nanPar1 - Tibetan frog - Nanorana parkeri
SEQ2_DIR=/hive/data/genomes/nanPar1/nanPar1.2bit
SEQ2_LEN=/hive/data/genomes/nanPar1/chrom.sizes
SEQ2_CHUNK=1000000
SEQ2_LIMIT=2000
SEQ2_LAP=0

BASE=/hive/data/genomes/galGal6/bed/lastzNanPar1.2018-10-20
TMPDIR=/dev/shm
" > DEF

    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
      -workhorse=hgwdev -bigClusterHub=ku \
        -dbHost=hgwdev -smallClusterHub=ku \
          -fileServer=hgwdev -syntenicNet) > do.log 2>&1
    # real	246m50.610s

    cat fb.galGal6.chainNanPar1Link.txt
    # 79844603 bases of 1055588482 (7.564%) in intersection

    cat fb.galGal6.chainSynNanPar1Link.txt
    # 32681061 bases of 1055588482 (3.096%) in intersection

    time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \
	galGal6 NanPar1) > rbest.log 2>&1 &
    # real	114m3.839s

    cat fb.galGal6.chainRBest.NanPar1.txt
    # 60765484 bases of 1055588482 (5.757%) in intersection

#############################################################################
# LASTZ chicken/galGal6 vs Crested ibis/nipNip1 - (DONE - 2018-10-20 - script/hiram)
    mkdir /hive/data/genomes/galGal6/bed/lastzNipNip1.2018-10-20
    cd /hive/data/genomes/galGal6/bed/lastzNipNip1.2018-10-20

   printf "# chicken vs Crested ibis
# galGal6 vs nipNip1
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.00/bin/lastz
BLASTZ_H=2000
BLASTZ_Y=3400
BLASTZ_L=4000
BLASTZ_K=2200
BLASTZ_M=254
BLASTZ_Q=/cluster/data/blastz/HoxD55.q

# TARGET: galGal6 - chicken - Gallus gallus
SEQ1_DIR=/hive/data/genomes/galGal6/galGal6.2bit
SEQ1_LEN=/hive/data/genomes/galGal6/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
SEQ1_LIMIT=40

# QUERY: nipNip1 - Crested ibis - Nipponia nippon
SEQ2_DIR=/hive/data/genomes/nipNip1/nipNip1.2bit
SEQ2_LEN=/hive/data/genomes/nipNip1/chrom.sizes
SEQ2_CHUNK=1000000
SEQ2_LIMIT=2000
SEQ2_LAP=0

BASE=/hive/data/genomes/galGal6/bed/lastzNipNip1.2018-10-20
TMPDIR=/dev/shm
" > DEF

    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
      -workhorse=hgwdev -bigClusterHub=ku \
        -dbHost=hgwdev -smallClusterHub=ku \
          -fileServer=hgwdev -syntenicNet) > do.log 2>&1
    # real	468m6.512s

    cat fb.galGal6.chainNipNip1Link.txt
    # 917340936 bases of 1055588482 (86.903%) in intersection

    cat fb.galGal6.chainSynNipNip1Link.txt
    # 816164720 bases of 1055588482 (77.318%) in intersection

    time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \
	galGal6 NipNip1) > rbest.log 2>&1 &
    # real	258m34.526s

    cat fb.galGal6.chainRBest.NipNip1.txt
    # 839113287 bases of 1055588482 (79.492%) in intersection

#############################################################################
# LASTZ chicken/galGal6 vs Hoatzin/opiHoa1 - (DONE - 2018-10-20 - script/hiram)
    mkdir /hive/data/genomes/galGal6/bed/lastzOpiHoa1.2018-10-20
    cd /hive/data/genomes/galGal6/bed/lastzOpiHoa1.2018-10-20

   printf "# chicken vs Hoatzin
# galGal6 vs opiHoa1
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.00/bin/lastz
BLASTZ_H=2000
BLASTZ_Y=3400
BLASTZ_L=4000
BLASTZ_K=2200
BLASTZ_M=254
BLASTZ_Q=/cluster/data/blastz/HoxD55.q

# TARGET: galGal6 - chicken - Gallus gallus
SEQ1_DIR=/hive/data/genomes/galGal6/galGal6.2bit
SEQ1_LEN=/hive/data/genomes/galGal6/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
SEQ1_LIMIT=40

# QUERY: opiHoa1 - Hoatzin - Opisthocomus hoazin
SEQ2_DIR=/hive/data/genomes/opiHoa1/opiHoa1.2bit
SEQ2_LEN=/hive/data/genomes/opiHoa1/chrom.sizes
SEQ2_CHUNK=1000000
SEQ2_LIMIT=2000
SEQ2_LAP=0

BASE=/hive/data/genomes/galGal6/bed/lastzOpiHoa1.2018-10-20
TMPDIR=/dev/shm
" > DEF

    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
      -workhorse=hgwdev -bigClusterHub=ku \
        -dbHost=hgwdev -smallClusterHub=ku \
          -fileServer=hgwdev -syntenicNet) > do.log 2>&1
    # real	489m5.171s

    cat fb.galGal6.chainOpiHoa1Link.txt
    # 892802003 bases of 1055588482 (84.579%) in intersection

    cat fb.galGal6.chainSynOpiHoa1Link.txt
    # 789312550 bases of 1055588482 (74.775%) in intersection

    time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \
	galGal6 OpiHoa1) > rbest.log 2>&1 &
    # real	283m23.426s

    cat fb.galGal6.chainRBest.OpiHoa1.txt
    # 810599536 bases of 1055588482 (76.791%) in intersection

#############################################################################
# LASTZ chicken/galGal6 vs Nile tilapia/oreNil3 - (DONE - 2018-10-20 - script/hiram)
    mkdir /hive/data/genomes/galGal6/bed/lastzOreNil3.2018-10-20
    cd /hive/data/genomes/galGal6/bed/lastzOreNil3.2018-10-20

   printf "# chicken vs Nile tilapia
# galGal6 vs oreNil3
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.00/bin/lastz
BLASTZ_H=2000
BLASTZ_Y=3400
BLASTZ_L=4000
BLASTZ_K=2200
BLASTZ_M=254
BLASTZ_Q=/cluster/data/blastz/HoxD55.q

# TARGET: galGal6 - chicken - Gallus gallus
SEQ1_DIR=/hive/data/genomes/galGal6/galGal6.2bit
SEQ1_LEN=/hive/data/genomes/galGal6/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
SEQ1_LIMIT=40

# QUERY: oreNil3 - Nile tilapia - Oreochromis niloticus
SEQ2_DIR=/hive/data/genomes/oreNil3/oreNil3.2bit
SEQ2_LEN=/hive/data/genomes/oreNil3/chrom.sizes
SEQ2_CHUNK=1000000
SEQ2_LIMIT=2000
SEQ2_LAP=0

BASE=/hive/data/genomes/galGal6/bed/lastzOreNil3.2018-10-20
TMPDIR=/dev/shm
" > DEF

    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
      -workhorse=hgwdev -bigClusterHub=ku \
        -dbHost=hgwdev -smallClusterHub=ku \
          -fileServer=hgwdev -syntenicNet) > do.log 2>&1
    # real	145m20.448s

    cat fb.galGal6.chainOreNil3Link.txt
    # 51982658 bases of 1055588482 (4.925%) in intersection

    cat fb.galGal6.chainSynOreNil3Link.txt
    # 15123869 bases of 1055588482 (1.433%) in intersection

    time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \
	galGal6 OreNil3) > rbest.log 2>&1 &
    # real	109m35.337s

    cat fb.galGal6.chainRBest.OreNil3.txt
    # 42938334 bases of 1055588482 (4.068%) in intersection

#############################################################################
# LASTZ chicken/galGal6 vs Medaka/oryLat2 - (DONE - 2018-10-20 - script/hiram)
    mkdir /hive/data/genomes/galGal6/bed/lastzOryLat2.2018-10-20
    cd /hive/data/genomes/galGal6/bed/lastzOryLat2.2018-10-20

   printf "# chicken vs Medaka
# galGal6 vs oryLat2
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.00/bin/lastz
BLASTZ_H=2000
BLASTZ_Y=3400
BLASTZ_L=4000
BLASTZ_K=2200
BLASTZ_M=254
BLASTZ_Q=/cluster/data/blastz/HoxD55.q

# TARGET: galGal6 - chicken - Gallus gallus
SEQ1_DIR=/hive/data/genomes/galGal6/galGal6.2bit
SEQ1_LEN=/hive/data/genomes/galGal6/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
SEQ1_LIMIT=40

# QUERY: oryLat2 - Medaka - Oryzias latipes
SEQ2_DIR=/hive/data/genomes/oryLat2/oryLat2.2bit
SEQ2_LEN=/hive/data/genomes/oryLat2/chrom.sizes
SEQ2_CHUNK=1000000
SEQ2_LIMIT=2000
SEQ2_LAP=0

BASE=/hive/data/genomes/galGal6/bed/lastzOryLat2.2018-10-20
TMPDIR=/dev/shm
" > DEF

    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
      -workhorse=hgwdev -bigClusterHub=ku \
        -dbHost=hgwdev -smallClusterHub=ku \
          -fileServer=hgwdev -syntenicNet) > do.log 2>&1
    # real	115m40.641s

    cat fb.galGal6.chainOryLat2Link.txt
    # 48185568 bases of 1055588482 (4.565%) in intersection

    cat fb.galGal6.chainSynOryLat2Link.txt
    # 12103669 bases of 1055588482 (1.147%) in intersection

    time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \
	galGal6 OryLat2) > rbest.log 2>&1 &
    # real	86m59.599s

    cat fb.galGal6.chainRBest.OryLat2.txt
    # 37955179 bases of 1055588482 (3.596%) in intersection

#############################################################################
# LASTZ chicken/galGal6 vs Dalmatian pelican/pelCri1 - (DONE - 2018-10-20 - script/hiram)
    mkdir /hive/data/genomes/galGal6/bed/lastzPelCri1.2018-10-20
    cd /hive/data/genomes/galGal6/bed/lastzPelCri1.2018-10-20

   printf "# chicken vs Dalmatian pelican
# galGal6 vs pelCri1
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.00/bin/lastz
BLASTZ_H=2000
BLASTZ_Y=3400
BLASTZ_L=4000
BLASTZ_K=2200
BLASTZ_M=254
BLASTZ_Q=/cluster/data/blastz/HoxD55.q

# TARGET: galGal6 - chicken - Gallus gallus
SEQ1_DIR=/hive/data/genomes/galGal6/galGal6.2bit
SEQ1_LEN=/hive/data/genomes/galGal6/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
SEQ1_LIMIT=40

# QUERY: pelCri1 - Dalmatian pelican - Pelecanus crispus
SEQ2_DIR=/hive/data/genomes/pelCri1/pelCri1.2bit
SEQ2_LEN=/hive/data/genomes/pelCri1/chrom.sizes
SEQ2_CHUNK=1000000
SEQ2_LIMIT=2000
SEQ2_LAP=0

BASE=/hive/data/genomes/galGal6/bed/lastzPelCri1.2018-10-20
TMPDIR=/dev/shm
" > DEF

    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
      -workhorse=hgwdev -bigClusterHub=ku \
        -dbHost=hgwdev -smallClusterHub=ku \
          -fileServer=hgwdev -syntenicNet) > do.log 2>&1
    # real	448m45.276s

    cat fb.galGal6.chainPelCri1Link.txt
    # 900882646 bases of 1055588482 (85.344%) in intersection

    cat fb.galGal6.chainSynPelCri1Link.txt
    # 761992182 bases of 1055588482 (72.186%) in intersection

    time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \
	galGal6 PelCri1) > rbest.log 2>&1 &
    # real	321m51.723s

    cat fb.galGal6.chainRBest.PelCri1.txt
    # 825489194 bases of 1055588482 (78.202%) in intersection

#############################################################################
# LASTZ chicken/galGal6 vs Chinese softshell turtle/pelSin1 - (DONE - 2018-10-20 - script/hiram)
    mkdir /hive/data/genomes/galGal6/bed/lastzPelSin1.2018-10-20
    cd /hive/data/genomes/galGal6/bed/lastzPelSin1.2018-10-20

   printf "# chicken vs Chinese softshell turtle
# galGal6 vs pelSin1
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.00/bin/lastz
BLASTZ_H=2000
BLASTZ_Y=3400
BLASTZ_L=4000
BLASTZ_K=2200
BLASTZ_M=254
BLASTZ_Q=/cluster/data/blastz/HoxD55.q

# TARGET: galGal6 - chicken - Gallus gallus
SEQ1_DIR=/hive/data/genomes/galGal6/galGal6.2bit
SEQ1_LEN=/hive/data/genomes/galGal6/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
SEQ1_LIMIT=40

# QUERY: pelSin1 - Chinese softshell turtle - Pelodiscus sinensis
SEQ2_DIR=/hive/data/genomes/pelSin1/pelSin1.2bit
SEQ2_LEN=/hive/data/genomes/pelSin1/chrom.sizes
SEQ2_CHUNK=1000000
SEQ2_LIMIT=2000
SEQ2_LAP=0

BASE=/hive/data/genomes/galGal6/bed/lastzPelSin1.2018-10-20
TMPDIR=/dev/shm
" > DEF

    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
      -workhorse=hgwdev -bigClusterHub=ku \
        -dbHost=hgwdev -smallClusterHub=ku \
          -fileServer=hgwdev -syntenicNet) > do.log 2>&1
    # real	606m19.155s

    cat fb.galGal6.chainPelSin1Link.txt
    # 443193142 bases of 1055588482 (41.985%) in intersection

    cat fb.galGal6.chainSynPelSin1Link.txt
    # 328819719 bases of 1055588482 (31.150%) in intersection

    time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \
	galGal6 PelSin1) > rbest.log 2>&1 &
    # real	462m36.209s

    cat fb.galGal6.chainRBest.PelSin1.txt
    # 379282279 bases of 1055588482 (35.931%) in intersection

#############################################################################
# LASTZ chicken/galGal6 vs Great cormorant/phaCar1 - (DONE - 2018-10-20 - script/hiram)
    mkdir /hive/data/genomes/galGal6/bed/lastzPhaCar1.2018-10-20
    cd /hive/data/genomes/galGal6/bed/lastzPhaCar1.2018-10-20

   printf "# chicken vs Great cormorant
# galGal6 vs phaCar1
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.00/bin/lastz
BLASTZ_H=2000
BLASTZ_Y=3400
BLASTZ_L=4000
BLASTZ_K=2200
BLASTZ_M=254
BLASTZ_Q=/cluster/data/blastz/HoxD55.q

# TARGET: galGal6 - chicken - Gallus gallus
SEQ1_DIR=/hive/data/genomes/galGal6/galGal6.2bit
SEQ1_LEN=/hive/data/genomes/galGal6/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
SEQ1_LIMIT=40

# QUERY: phaCar1 - Great cormorant - Phalacrocorax carbo
SEQ2_DIR=/hive/data/genomes/phaCar1/phaCar1.2bit
SEQ2_LEN=/hive/data/genomes/phaCar1/chrom.sizes
SEQ2_CHUNK=1000000
SEQ2_LIMIT=2000
SEQ2_LAP=0

BASE=/hive/data/genomes/galGal6/bed/lastzPhaCar1.2018-10-20
TMPDIR=/dev/shm
" > DEF

    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
      -workhorse=hgwdev -bigClusterHub=ku \
        -dbHost=hgwdev -smallClusterHub=ku \
          -fileServer=hgwdev -syntenicNet) > do.log 2>&1
    # real	521m40.317s

    cat fb.galGal6.chainPhaCar1Link.txt
    # 888618683 bases of 1055588482 (84.182%) in intersection

    cat fb.galGal6.chainSynPhaCar1Link.txt
    # 748304742 bases of 1055588482 (70.890%) in intersection

    time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \
	galGal6 PhaCar1) > rbest.log 2>&1 &
    # real	336m56.098s

    cat fb.galGal6.chainRBest.PhaCar1.txt
    # 812143245 bases of 1055588482 (76.937%) in intersection

#############################################################################
# LASTZ chicken/galGal6 vs White-tailed tropicbird/phaLep1 - (DONE - 2018-10-20 - script/hiram)
    mkdir /hive/data/genomes/galGal6/bed/lastzPhaLep1.2018-10-20
    cd /hive/data/genomes/galGal6/bed/lastzPhaLep1.2018-10-20

   printf "# chicken vs White-tailed tropicbird
# galGal6 vs phaLep1
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.00/bin/lastz
BLASTZ_H=2000
BLASTZ_Y=3400
BLASTZ_L=4000
BLASTZ_K=2200
BLASTZ_M=254
BLASTZ_Q=/cluster/data/blastz/HoxD55.q

# TARGET: galGal6 - chicken - Gallus gallus
SEQ1_DIR=/hive/data/genomes/galGal6/galGal6.2bit
SEQ1_LEN=/hive/data/genomes/galGal6/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
SEQ1_LIMIT=40

# QUERY: phaLep1 - White-tailed tropicbird - Phaethon lepturus
SEQ2_DIR=/hive/data/genomes/phaLep1/phaLep1.2bit
SEQ2_LEN=/hive/data/genomes/phaLep1/chrom.sizes
SEQ2_CHUNK=1000000
SEQ2_LIMIT=2000
SEQ2_LAP=0

BASE=/hive/data/genomes/galGal6/bed/lastzPhaLep1.2018-10-20
TMPDIR=/dev/shm
" > DEF

    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
      -workhorse=hgwdev -bigClusterHub=ku \
        -dbHost=hgwdev -smallClusterHub=ku \
          -fileServer=hgwdev -syntenicNet) > do.log 2>&1
    # real	522m18.477s

    cat fb.galGal6.chainPhaLep1Link.txt
    # 892174920 bases of 1055588482 (84.519%) in intersection

    cat fb.galGal6.chainSynPhaLep1Link.txt
    # 748102047 bases of 1055588482 (70.871%) in intersection

    time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \
	galGal6 PhaLep1) > rbest.log 2>&1 &
    # real	348m19.903s

    cat fb.galGal6.chainRBest.PhaLep1.txt
    # 815574374 bases of 1055588482 (77.263%) in intersection

#############################################################################
# LASTZ chicken/galGal6 vs American flamingo/phoRub1 - (DONE - 2018-10-21 - script/hiram)
    mkdir /hive/data/genomes/galGal6/bed/lastzPhoRub1.2018-10-21
    cd /hive/data/genomes/galGal6/bed/lastzPhoRub1.2018-10-21

   printf "# chicken vs American flamingo
# galGal6 vs phoRub1
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.00/bin/lastz
BLASTZ_H=2000
BLASTZ_Y=3400
BLASTZ_L=4000
BLASTZ_K=2200
BLASTZ_M=254
BLASTZ_Q=/cluster/data/blastz/HoxD55.q

# TARGET: galGal6 - chicken - Gallus gallus
SEQ1_DIR=/hive/data/genomes/galGal6/galGal6.2bit
SEQ1_LEN=/hive/data/genomes/galGal6/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
SEQ1_LIMIT=40

# QUERY: phoRub1 - American flamingo - Phoenicopterus ruber ruber
SEQ2_DIR=/hive/data/genomes/phoRub1/phoRub1.2bit
SEQ2_LEN=/hive/data/genomes/phoRub1/chrom.sizes
SEQ2_CHUNK=1000000
SEQ2_LIMIT=2000
SEQ2_LAP=0

BASE=/hive/data/genomes/galGal6/bed/lastzPhoRub1.2018-10-21
TMPDIR=/dev/shm
" > DEF

    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
      -workhorse=hgwdev -bigClusterHub=ku \
        -dbHost=hgwdev -smallClusterHub=ku \
          -fileServer=hgwdev -syntenicNet) > do.log 2>&1
    # real	453m3.724s

    cat fb.galGal6.chainPhoRub1Link.txt
    # 895062456 bases of 1055588482 (84.793%) in intersection

    cat fb.galGal6.chainSynPhoRub1Link.txt
    # 747746047 bases of 1055588482 (70.837%) in intersection

    time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \
	galGal6 PhoRub1) > rbest.log 2>&1 &
    # real	320m1.593s

    cat fb.galGal6.chainRBest.PhoRub1.txt
    # 820973879 bases of 1055588482 (77.774%) in intersection

#############################################################################
# LASTZ chicken/galGal6 vs Downy woodpecker/picPub1 - (DONE - 2018-10-21 - script/hiram)
    mkdir /hive/data/genomes/galGal6/bed/lastzPicPub1.2018-10-21
    cd /hive/data/genomes/galGal6/bed/lastzPicPub1.2018-10-21

   printf "# chicken vs Downy woodpecker
# galGal6 vs picPub1
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.00/bin/lastz
BLASTZ_H=2000
BLASTZ_Y=3400
BLASTZ_L=4000
BLASTZ_K=2200
BLASTZ_M=254
BLASTZ_Q=/cluster/data/blastz/HoxD55.q

# TARGET: galGal6 - chicken - Gallus gallus
SEQ1_DIR=/hive/data/genomes/galGal6/galGal6.2bit
SEQ1_LEN=/hive/data/genomes/galGal6/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
SEQ1_LIMIT=40

# QUERY: picPub1 - Downy woodpecker - Picoides pubescens
SEQ2_DIR=/hive/data/genomes/picPub1/picPub1.2bit
SEQ2_LEN=/hive/data/genomes/picPub1/chrom.sizes
SEQ2_CHUNK=1000000
SEQ2_LIMIT=2000
SEQ2_LAP=0

BASE=/hive/data/genomes/galGal6/bed/lastzPicPub1.2018-10-21
TMPDIR=/dev/shm
" > DEF

    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
      -workhorse=hgwdev -bigClusterHub=ku \
        -dbHost=hgwdev -smallClusterHub=ku \
          -fileServer=hgwdev -syntenicNet) > do.log 2>&1
    # real	707m2.631s

    cat fb.galGal6.chainPicPub1Link.txt
    # 783855965 bases of 1055588482 (74.258%) in intersection

    cat fb.galGal6.chainSynPicPub1Link.txt
    # 638057644 bases of 1055588482 (60.446%) in intersection

    time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \
	galGal6 PicPub1) > rbest.log 2>&1 &
    # real	557m15.590s

    cat fb.galGal6.chainRBest.PicPub1.txt
    # 673786174 bases of 1055588482 (63.830%) in intersection

#############################################################################
# LASTZ chicken/galGal6 vs Tibetan ground jay/pseHum1 - (DONE - 2018-10-21 - script/hiram)
    mkdir /hive/data/genomes/galGal6/bed/lastzPseHum1.2018-10-21
    cd /hive/data/genomes/galGal6/bed/lastzPseHum1.2018-10-21

   printf "# chicken vs Tibetan ground jay
# galGal6 vs pseHum1
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.00/bin/lastz
BLASTZ_H=2000
BLASTZ_Y=3400
BLASTZ_L=4000
BLASTZ_K=2200
BLASTZ_M=254
BLASTZ_Q=/cluster/data/blastz/HoxD55.q

# TARGET: galGal6 - chicken - Gallus gallus
SEQ1_DIR=/hive/data/genomes/galGal6/galGal6.2bit
SEQ1_LEN=/hive/data/genomes/galGal6/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
SEQ1_LIMIT=40

# QUERY: pseHum1 - Tibetan ground jay - Pseudopodoces humilis
SEQ2_DIR=/hive/data/genomes/pseHum1/pseHum1.2bit
SEQ2_LEN=/hive/data/genomes/pseHum1/chrom.sizes
SEQ2_CHUNK=1000000
SEQ2_LIMIT=2000
SEQ2_LAP=0

BASE=/hive/data/genomes/galGal6/bed/lastzPseHum1.2018-10-21
TMPDIR=/dev/shm
" > DEF

    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
      -workhorse=hgwdev -bigClusterHub=ku \
        -dbHost=hgwdev -smallClusterHub=ku \
          -fileServer=hgwdev -syntenicNet) > do.log 2>&1
    # real	657m45.610s

    cat fb.galGal6.chainPseHum1Link.txt
    # 851036997 bases of 1055588482 (80.622%) in intersection

    cat fb.galGal6.chainSynPseHum1Link.txt
    # 717648839 bases of 1055588482 (67.986%) in intersection

    time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \
	galGal6 PseHum1) > rbest.log 2>&1 &
    # real	478m33.407s

    cat fb.galGal6.chainRBest.PseHum1.txt
    # 747040317 bases of 1055588482 (70.770%) in intersection

#############################################################################
# LASTZ chicken/galGal6 vs Yellow-throated sandgrouse/pteGut1 - (DONE - 2018-10-21 - script/hiram)
    mkdir /hive/data/genomes/galGal6/bed/lastzPteGut1.2018-10-21
    cd /hive/data/genomes/galGal6/bed/lastzPteGut1.2018-10-21

   printf "# chicken vs Yellow-throated sandgrouse
# galGal6 vs pteGut1
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.00/bin/lastz
BLASTZ_H=2000
BLASTZ_Y=3400
BLASTZ_L=4000
BLASTZ_K=2200
BLASTZ_M=254
BLASTZ_Q=/cluster/data/blastz/HoxD55.q

# TARGET: galGal6 - chicken - Gallus gallus
SEQ1_DIR=/hive/data/genomes/galGal6/galGal6.2bit
SEQ1_LEN=/hive/data/genomes/galGal6/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
SEQ1_LIMIT=40

# QUERY: pteGut1 - Yellow-throated sandgrouse - Pterocles gutturalis
SEQ2_DIR=/hive/data/genomes/pteGut1/pteGut1.2bit
SEQ2_LEN=/hive/data/genomes/pteGut1/chrom.sizes
SEQ2_CHUNK=1000000
SEQ2_LIMIT=2000
SEQ2_LAP=0

BASE=/hive/data/genomes/galGal6/bed/lastzPteGut1.2018-10-21
TMPDIR=/dev/shm
" > DEF

    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
      -workhorse=hgwdev -bigClusterHub=ku \
        -dbHost=hgwdev -smallClusterHub=ku \
          -fileServer=hgwdev -syntenicNet) > do.log 2>&1
    # real	484m8.206s

    cat fb.galGal6.chainPteGut1Link.txt
    # 871105195 bases of 1055588482 (82.523%) in intersection

    cat fb.galGal6.chainSynPteGut1Link.txt
    # 727109988 bases of 1055588482 (68.882%) in intersection

    time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \
	galGal6 PteGut1) > rbest.log 2>&1 &
    # real	344m37.225s

    cat fb.galGal6.chainRBest.PteGut1.txt
    # 784577743 bases of 1055588482 (74.326%) in intersection

#############################################################################
# LASTZ chicken/galGal6 vs Adelie penguin/pygAde1 - (DONE - 2018-10-21 - script/hiram)
    mkdir /hive/data/genomes/galGal6/bed/lastzPygAde1.2018-10-21
    cd /hive/data/genomes/galGal6/bed/lastzPygAde1.2018-10-21

   printf "# chicken vs Adelie penguin
# galGal6 vs pygAde1
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.00/bin/lastz
BLASTZ_H=2000
BLASTZ_Y=3400
BLASTZ_L=4000
BLASTZ_K=2200
BLASTZ_M=254
BLASTZ_Q=/cluster/data/blastz/HoxD55.q

# TARGET: galGal6 - chicken - Gallus gallus
SEQ1_DIR=/hive/data/genomes/galGal6/galGal6.2bit
SEQ1_LEN=/hive/data/genomes/galGal6/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
SEQ1_LIMIT=40

# QUERY: pygAde1 - Adelie penguin - Pygoscelis adeliae
SEQ2_DIR=/hive/data/genomes/pygAde1/pygAde1.2bit
SEQ2_LEN=/hive/data/genomes/pygAde1/chrom.sizes
SEQ2_CHUNK=1000000
SEQ2_LIMIT=2000
SEQ2_LAP=0

BASE=/hive/data/genomes/galGal6/bed/lastzPygAde1.2018-10-21
TMPDIR=/dev/shm
" > DEF

    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
      -workhorse=hgwdev -bigClusterHub=ku \
        -dbHost=hgwdev -smallClusterHub=ku \
          -fileServer=hgwdev -syntenicNet) > do.log 2>&1
    # real	375m37.220s

    cat fb.galGal6.chainPygAde1Link.txt
    # 906663676 bases of 1055588482 (85.892%) in intersection

    cat fb.galGal6.chainSynPygAde1Link.txt
    # 820549396 bases of 1055588482 (77.734%) in intersection

    time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \
	galGal6 PygAde1) > rbest.log 2>&1 &
    # real	225m31.093s

    cat fb.galGal6.chainRBest.PygAde1.txt
    # 832234764 bases of 1055588482 (78.841%) in intersection

#############################################################################
# LASTZ chicken/galGal6 vs Burmese python/pytBiv1 - (DONE - 2018-10-21 - script/hiram)
    mkdir /hive/data/genomes/galGal6/bed/lastzPytBiv1.2018-10-21
    cd /hive/data/genomes/galGal6/bed/lastzPytBiv1.2018-10-21

   printf "# chicken vs Burmese python
# galGal6 vs pytBiv1
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.00/bin/lastz
BLASTZ_H=2000
BLASTZ_Y=3400
BLASTZ_L=4000
BLASTZ_K=2200
BLASTZ_M=254
BLASTZ_Q=/cluster/data/blastz/HoxD55.q

# TARGET: galGal6 - chicken - Gallus gallus
SEQ1_DIR=/hive/data/genomes/galGal6/galGal6.2bit
SEQ1_LEN=/hive/data/genomes/galGal6/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
SEQ1_LIMIT=40

# QUERY: pytBiv1 - Burmese python - Python bivittatus
SEQ2_DIR=/hive/data/genomes/pytBiv1/pytBiv1.2bit
SEQ2_LEN=/hive/data/genomes/pytBiv1/chrom.sizes
SEQ2_CHUNK=1000000
SEQ2_LIMIT=2000
SEQ2_LAP=0

BASE=/hive/data/genomes/galGal6/bed/lastzPytBiv1.2018-10-21
TMPDIR=/dev/shm
" > DEF

    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
      -workhorse=hgwdev -bigClusterHub=ku \
        -dbHost=hgwdev -smallClusterHub=ku \
          -fileServer=hgwdev -syntenicNet) > do.log 2>&1
    # real	324m31.677s

    cat fb.galGal6.chainPytBiv1Link.txt
    # 166849799 bases of 1055588482 (15.806%) in intersection

    cat fb.galGal6.chainSynPytBiv1Link.txt
    # 71801031 bases of 1055588482 (6.802%) in intersection

    time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \
	galGal6 PytBiv1) > rbest.log 2>&1 &
    # real	268m26.640s

    cat fb.galGal6.chainRBest.PytBiv1.txt
    # 125015534 bases of 1055588482 (11.843%) in intersection

#############################################################################
# LASTZ chicken/galGal6 vs Canary/serCan1 - (DONE - 2018-10-21 - script/hiram)
    mkdir /hive/data/genomes/galGal6/bed/lastzSerCan1.2018-10-21
    cd /hive/data/genomes/galGal6/bed/lastzSerCan1.2018-10-21

   printf "# chicken vs Canary
# galGal6 vs serCan1
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.00/bin/lastz
BLASTZ_H=2000
BLASTZ_Y=3400
BLASTZ_L=4000
BLASTZ_K=2200
BLASTZ_M=254
BLASTZ_Q=/cluster/data/blastz/HoxD55.q

# TARGET: galGal6 - chicken - Gallus gallus
SEQ1_DIR=/hive/data/genomes/galGal6/galGal6.2bit
SEQ1_LEN=/hive/data/genomes/galGal6/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
SEQ1_LIMIT=40

# QUERY: serCan1 - Canary - Serinus canaria
SEQ2_DIR=/hive/data/genomes/serCan1/serCan1.2bit
SEQ2_LEN=/hive/data/genomes/serCan1/chrom.sizes
SEQ2_CHUNK=1000000
SEQ2_LIMIT=2000
SEQ2_LAP=0

BASE=/hive/data/genomes/galGal6/bed/lastzSerCan1.2018-10-21
TMPDIR=/dev/shm
" > DEF

    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
      -workhorse=hgwdev -bigClusterHub=ku \
        -dbHost=hgwdev -smallClusterHub=ku \
          -fileServer=hgwdev -syntenicNet) > do.log 2>&1
    # real	717m30.966s

    cat fb.galGal6.chainSerCan1Link.txt
    # 843441693 bases of 1055588482 (79.903%) in intersection

    cat fb.galGal6.chainSynSerCan1Link.txt
    # 699854918 bases of 1055588482 (66.300%) in intersection

    time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \
	galGal6 SerCan1) > rbest.log 2>&1 &
    # real	522m59.796s

    cat fb.galGal6.chainRBest.SerCan1.txt
    # 733176559 bases of 1055588482 (69.457%) in intersection

#############################################################################
# LASTZ chicken/galGal6 vs Ostrich/strCam1 - (DONE - 2018-10-21 - script/hiram)
    mkdir /hive/data/genomes/galGal6/bed/lastzStrCam1.2018-10-21
    cd /hive/data/genomes/galGal6/bed/lastzStrCam1.2018-10-21

   printf "# chicken vs Ostrich
# galGal6 vs strCam1
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.00/bin/lastz
BLASTZ_H=2000
BLASTZ_Y=3400
BLASTZ_L=4000
BLASTZ_K=2200
BLASTZ_M=254
BLASTZ_Q=/cluster/data/blastz/HoxD55.q

# TARGET: galGal6 - chicken - Gallus gallus
SEQ1_DIR=/hive/data/genomes/galGal6/galGal6.2bit
SEQ1_LEN=/hive/data/genomes/galGal6/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
SEQ1_LIMIT=40

# QUERY: strCam1 - Ostrich - Struthio camelus australis
SEQ2_DIR=/hive/data/genomes/strCam1/strCam1.2bit
SEQ2_LEN=/hive/data/genomes/strCam1/chrom.sizes
SEQ2_CHUNK=1000000
SEQ2_LIMIT=2000
SEQ2_LAP=0

BASE=/hive/data/genomes/galGal6/bed/lastzStrCam1.2018-10-21
TMPDIR=/dev/shm
" > DEF

    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
      -workhorse=hgwdev -bigClusterHub=ku \
        -dbHost=hgwdev -smallClusterHub=ku \
          -fileServer=hgwdev -syntenicNet) > do.log 2>&1
    # real	363m35.472s

    cat fb.galGal6.chainStrCam1Link.txt
    # 869691537 bases of 1055588482 (82.389%) in intersection

    cat fb.galGal6.chainSynStrCam1Link.txt
    # 787385857 bases of 1055588482 (74.592%) in intersection

    time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \
	galGal6 StrCam1) > rbest.log 2>&1 &
    # real	205m25.277s

    cat fb.galGal6.chainRBest.StrCam1.txt
    # 800156430 bases of 1055588482 (75.802%) in intersection

#############################################################################
# LASTZ chicken/galGal6 vs Red crested turaco/tauEry1 - (DONE - 2018-10-21 - script/hiram)
    mkdir /hive/data/genomes/galGal6/bed/lastzTauEry1.2018-10-21
    cd /hive/data/genomes/galGal6/bed/lastzTauEry1.2018-10-21

   printf "# chicken vs Red crested turaco
# galGal6 vs tauEry1
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.00/bin/lastz
BLASTZ_H=2000
BLASTZ_Y=3400
BLASTZ_L=4000
BLASTZ_K=2200
BLASTZ_M=254
BLASTZ_Q=/cluster/data/blastz/HoxD55.q

# TARGET: galGal6 - chicken - Gallus gallus
SEQ1_DIR=/hive/data/genomes/galGal6/galGal6.2bit
SEQ1_LEN=/hive/data/genomes/galGal6/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
SEQ1_LIMIT=40

# QUERY: tauEry1 - Red crested turaco - Tauraco erythrolophus
SEQ2_DIR=/hive/data/genomes/tauEry1/tauEry1.2bit
SEQ2_LEN=/hive/data/genomes/tauEry1/chrom.sizes
SEQ2_CHUNK=1000000
SEQ2_LIMIT=2000
SEQ2_LAP=0

BASE=/hive/data/genomes/galGal6/bed/lastzTauEry1.2018-10-21
TMPDIR=/dev/shm
" > DEF

    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
      -workhorse=hgwdev -bigClusterHub=ku \
        -dbHost=hgwdev -smallClusterHub=ku \
          -fileServer=hgwdev -syntenicNet) > do.log 2>&1
    # real	479m16.276s

    cat fb.galGal6.chainTauEry1Link.txt
    # 891815531 bases of 1055588482 (84.485%) in intersection

    cat fb.galGal6.chainSynTauEry1Link.txt
    # 754044834 bases of 1055588482 (71.434%) in intersection

    time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \
	galGal6 TauEry1) > rbest.log 2>&1 &
    # real	315m40.917s

    cat fb.galGal6.chainRBest.TauEry1.txt
    # 810517802 bases of 1055588482 (76.784%) in intersection

#############################################################################
# LASTZ chicken/galGal6 vs Tetraodon/tetNig2 - (DONE - 2018-10-21 - script/hiram)
    mkdir /hive/data/genomes/galGal6/bed/lastzTetNig2.2018-10-21
    cd /hive/data/genomes/galGal6/bed/lastzTetNig2.2018-10-21

   printf "# chicken vs Tetraodon
# galGal6 vs tetNig2
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.00/bin/lastz
BLASTZ_H=2000
BLASTZ_Y=3400
BLASTZ_L=4000
BLASTZ_K=2200
BLASTZ_M=254
BLASTZ_Q=/cluster/data/blastz/HoxD55.q

# TARGET: galGal6 - chicken - Gallus gallus
SEQ1_DIR=/hive/data/genomes/galGal6/galGal6.2bit
SEQ1_LEN=/hive/data/genomes/galGal6/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
SEQ1_LIMIT=40

# QUERY: tetNig2 - Tetraodon - Tetraodon nigroviridis
SEQ2_DIR=/hive/data/genomes/tetNig2/tetNig2.2bit
SEQ2_LEN=/hive/data/genomes/tetNig2/chrom.sizes
SEQ2_CHUNK=1000000
SEQ2_LIMIT=2000
SEQ2_LAP=0

BASE=/hive/data/genomes/galGal6/bed/lastzTetNig2.2018-10-21
TMPDIR=/dev/shm
" > DEF

    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
      -workhorse=hgwdev -bigClusterHub=ku \
        -dbHost=hgwdev -smallClusterHub=ku \
          -fileServer=hgwdev -syntenicNet) > do.log 2>&1
    # real	103m2.026s

    cat fb.galGal6.chainTetNig2Link.txt
    # 43782179 bases of 1055588482 (4.148%) in intersection

    cat fb.galGal6.chainSynTetNig2Link.txt
    # 10673340 bases of 1055588482 (1.011%) in intersection

    time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \
	galGal6 TetNig2) > rbest.log 2>&1 &
    # real	68m58.779s

    cat fb.galGal6.chainRBest.TetNig2.txt
    # 32928708 bases of 1055588482 (3.119%) in intersection

#############################################################################
# LASTZ chicken/galGal6 vs Garter snake/thaSir1 - (DONE - 2018-10-21 - script/hiram)
    mkdir /hive/data/genomes/galGal6/bed/lastzThaSir1.2018-10-21
    cd /hive/data/genomes/galGal6/bed/lastzThaSir1.2018-10-21

   printf "# chicken vs Garter snake
# galGal6 vs thaSir1
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.00/bin/lastz
BLASTZ_H=2000
BLASTZ_Y=3400
BLASTZ_L=4000
BLASTZ_K=2200
BLASTZ_M=254
BLASTZ_Q=/cluster/data/blastz/HoxD55.q

# TARGET: galGal6 - chicken - Gallus gallus
SEQ1_DIR=/hive/data/genomes/galGal6/galGal6.2bit
SEQ1_LEN=/hive/data/genomes/galGal6/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
SEQ1_LIMIT=40

# QUERY: thaSir1 - Garter snake - Thamnophis sirtalis
SEQ2_DIR=/hive/data/genomes/thaSir1/thaSir1.2bit
SEQ2_LEN=/hive/data/genomes/thaSir1/chrom.sizes
SEQ2_CHUNK=1000000
SEQ2_LIMIT=2000
SEQ2_LAP=0

BASE=/hive/data/genomes/galGal6/bed/lastzThaSir1.2018-10-21
TMPDIR=/dev/shm
" > DEF

    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
      -workhorse=hgwdev -bigClusterHub=ku \
        -dbHost=hgwdev -smallClusterHub=ku \
          -fileServer=hgwdev -syntenicNet) > do.log 2>&1
    # real	263m16.804s

    cat fb.galGal6.chainThaSir1Link.txt
    # 124073447 bases of 1055588482 (11.754%) in intersection

    cat fb.galGal6.chainSynThaSir1Link.txt
    # 41632178 bases of 1055588482 (3.944%) in intersection

    time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \
	galGal6 ThaSir1) > rbest.log 2>&1 &
    # real	179m29.254s

    cat fb.galGal6.chainRBest.ThaSir1.txt
    # 93424295 bases of 1055588482 (8.850%) in intersection

#############################################################################
# LASTZ chicken/galGal6 vs Barn owl/tytAlb1 - (DONE - 2018-10-21 - script/hiram)
    mkdir /hive/data/genomes/galGal6/bed/lastzTytAlb1.2018-10-21
    cd /hive/data/genomes/galGal6/bed/lastzTytAlb1.2018-10-21

   printf "# chicken vs Barn owl
# galGal6 vs tytAlb1
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.00/bin/lastz
BLASTZ_H=2000
BLASTZ_Y=3400
BLASTZ_L=4000
BLASTZ_K=2200
BLASTZ_M=254
BLASTZ_Q=/cluster/data/blastz/HoxD55.q

# TARGET: galGal6 - chicken - Gallus gallus
SEQ1_DIR=/hive/data/genomes/galGal6/galGal6.2bit
SEQ1_LEN=/hive/data/genomes/galGal6/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
SEQ1_LIMIT=40

# QUERY: tytAlb1 - Barn owl - Tyto alba
SEQ2_DIR=/hive/data/genomes/tytAlb1/tytAlb1.2bit
SEQ2_LEN=/hive/data/genomes/tytAlb1/chrom.sizes
SEQ2_CHUNK=1000000
SEQ2_LIMIT=2000
SEQ2_LAP=0

BASE=/hive/data/genomes/galGal6/bed/lastzTytAlb1.2018-10-21
TMPDIR=/dev/shm
" > DEF

    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
      -workhorse=hgwdev -bigClusterHub=ku \
        -dbHost=hgwdev -smallClusterHub=ku \
          -fileServer=hgwdev -syntenicNet) > do.log 2>&1
    # real	510m12.860s

    cat fb.galGal6.chainTytAlb1Link.txt
    # 887980659 bases of 1055588482 (84.122%) in intersection

    cat fb.galGal6.chainSynTytAlb1Link.txt
    # 743212909 bases of 1055588482 (70.407%) in intersection

    time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \
	galGal6 TytAlb1) > rbest.log 2>&1 &
    # real	302m9.764s

    cat fb.galGal6.chainRBest.TytAlb1.txt
    # 804558618 bases of 1055588482 (76.219%) in intersection

#############################################################################
# LASTZ chicken/galGal6 vs African clawed frog/xenLae2 - (DONE - 2018-10-21 - script/hiram)
    mkdir /hive/data/genomes/galGal6/bed/lastzXenLae2.2018-10-21
    cd /hive/data/genomes/galGal6/bed/lastzXenLae2.2018-10-21

   printf "# chicken vs African clawed frog
# galGal6 vs xenLae2
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.00/bin/lastz
BLASTZ_H=2000
BLASTZ_Y=3400
BLASTZ_L=4000
BLASTZ_K=2200
BLASTZ_M=254
BLASTZ_Q=/cluster/data/blastz/HoxD55.q

# TARGET: galGal6 - chicken - Gallus gallus
SEQ1_DIR=/hive/data/genomes/galGal6/galGal6.2bit
SEQ1_LEN=/hive/data/genomes/galGal6/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
SEQ1_LIMIT=40

# QUERY: xenLae2 - African clawed frog - Xenopus laevis
SEQ2_DIR=/hive/data/genomes/xenLae2/xenLae2.2bit
SEQ2_LEN=/hive/data/genomes/xenLae2/chrom.sizes
SEQ2_CHUNK=1000000
SEQ2_LIMIT=2000
SEQ2_LAP=0

BASE=/hive/data/genomes/galGal6/bed/lastzXenLae2.2018-10-21
TMPDIR=/dev/shm
" > DEF

    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
      -workhorse=hgwdev -bigClusterHub=ku \
        -dbHost=hgwdev -smallClusterHub=ku \
          -fileServer=hgwdev -syntenicNet) > do.log 2>&1
    # real	391m11.899s

    cat fb.galGal6.chainXenLae2Link.txt
    # 83674239 bases of 1055588482 (7.927%) in intersection

    cat fb.galGal6.chainSynXenLae2Link.txt
    # 40258327 bases of 1055588482 (3.814%) in intersection

    time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \
	galGal6 XenLae2) > rbest.log 2>&1 &
    # real	242m24.342s

    cat fb.galGal6.chainRBest.XenLae2.txt
    # 69131006 bases of 1055588482 (6.549%) in intersection

#############################################################################
# LASTZ chicken/galGal6 vs Japanese quail/cotJap2 - (DONE - 2018-10-25 - script/hiram)
    mkdir /hive/data/genomes/galGal6/bed/lastzCotJap2.2018-10-25
    cd /hive/data/genomes/galGal6/bed/lastzCotJap2.2018-10-25

   printf "# chicken vs Japanese quail
# galGal6 vs cotJap2
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.00/bin/lastz
BLASTZ_H=2000
BLASTZ_Y=3400
BLASTZ_L=4000
BLASTZ_K=2200
BLASTZ_M=254
BLASTZ_Q=/cluster/data/blastz/HoxD55.q

# TARGET: galGal6 - chicken - Gallus gallus
SEQ1_DIR=/hive/data/genomes/galGal6/galGal6.2bit
SEQ1_LEN=/hive/data/genomes/galGal6/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
SEQ1_LIMIT=40

# QUERY: cotJap2 - Japanese quail - Coturnix japonica
SEQ2_DIR=/hive/data/genomes/cotJap2/cotJap2.2bit
SEQ2_LEN=/hive/data/genomes/cotJap2/chrom.sizes
SEQ2_CHUNK=1000000
SEQ2_LIMIT=2000
SEQ2_LAP=0

BASE=/hive/data/genomes/galGal6/bed/lastzCotJap2.2018-10-25
TMPDIR=/dev/shm
" > DEF

    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
      -workhorse=hgwdev -bigClusterHub=ku \
        -dbHost=hgwdev -smallClusterHub=ku \
          -fileServer=hgwdev -syntenicNet) > do.log 2>&1
    # real	402m14.191s

    cat fb.galGal6.chainCotJap2Link.txt
    # 950779519 bases of 1055588482 (90.071%) in intersection

    cat fb.galGal6.chainSynCotJap2Link.txt
    # 840595400 bases of 1055588482 (79.633%) in intersection

    time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \
	galGal6 CotJap2) > rbest.log 2>&1 &
    # real	331m41.351s

    cat fb.galGal6.chainRBest.CotJap2.txt
    # 846148712 bases of 1055588482 (80.159%) in intersection

    #   running the swap
    mkdir /hive/data/genomes/cotJap2/bed/blastz.galGal6.swap
    cd /hive/data/genomes/cotJap2/bed/blastz.galGal6.swap
    time (doBlastzChainNet.pl -verbose=2 \
        /hive/data/genomes/galGal6/bed/lastzBosTau9.2018-10-25/DEF \
        -swap  -syntenicNet -workhorse=hgwdev \
	-smallClusterHub=hgwdev-101 -bigClusterHub=ku \
        ) > swap.log 2>&1
    #   real    286m17.880s

    cat fb.cotJap2.chainGalGal6Link.txt
    #   883933933 bases of 917263224 (96.366%) in intersection
    cat fb.cotJap2.chainSynGalGal6Link.txt
    #	838388062 bases of 917263224 (91.401%) in intersection

    time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` cotJap2 galGal6) > rbest.log 2>&1 &

    cat fb.cotJap2.chainRBest.GalGal6.txt
    # 846862875 bases of 917263224 (92.325%) in intersection

#############################################################################
# LASTZ chicken/galGal6 vs Zebrafish/danRer10 - (DONE - 2020-02-25 - script/hiram)
    mkdir /hive/data/genomes/galGal6/bed/lastzDanRer10.2020-02-25
    cd /hive/data/genomes/galGal6/bed/lastzDanRer10.2020-02-25

   printf "# chicken vs Zebrafish
# galGal6 vs danRer10
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.00/bin/lastz
BLASTZ_H=2000
BLASTZ_Y=3400
BLASTZ_L=4000
BLASTZ_K=2200
BLASTZ_M=254
BLASTZ_Q=/cluster/data/blastz/HoxD55.q

# TARGET: galGal6 - chicken - Gallus gallus
SEQ1_DIR=/hive/data/genomes/galGal6/galGal6.2bit
SEQ1_LEN=/hive/data/genomes/galGal6/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
SEQ1_LIMIT=40

# QUERY: danRer10 - Zebrafish - Danio rerio
SEQ2_DIR=/hive/data/genomes/danRer10/danRer10.2bit
SEQ2_LEN=/hive/data/genomes/danRer10/chrom.sizes
SEQ2_CHUNK=1000000
SEQ2_LIMIT=2000
SEQ2_LAP=0

BASE=/hive/data/genomes/galGal6/bed/lastzDanRer10.2020-02-25
TMPDIR=/dev/shm
" > DEF

    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
      -workhorse=hgwdev -bigClusterHub=ku \
        -dbHost=hgwdev -smallClusterHub=ku \
          -fileServer=hgwdev -syntenicNet) > do.log 2>&1
    # real    156m19.439s

    cat fb.galGal6.chainDanRer10Link.txt
    # 65140381 bases of 1055588482 (6.171%) in intersection

    cat fb.galGal6.chainSynDanRer10Link.txt
    # 14892321 bases of 1055588482 (1.411%) in intersection

    time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \
	galGal6 danRer10) > rbest.log 2>&1 &
    # real	181m30.518s

    cat fb.galGal6.chainRBest.DanRer10.txt
    # 54759431 bases of 1055588482 (5.188%) in intersection

    mkdir /hive/data/genomes/danRer10/bed/blastz.galGal6.swap
    cd /hive/data/genomes/danRer10/bed/blastz.galGal6.swap

    time (doBlastzChainNet.pl -verbose=2 \
	/hive/data/genomes/galGal6/bed/lastzDanRer10.2020-02-25/DEF \
	-workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
	-syntenicNet -swap) > swap.log 2>&1 &
    #	real    6m15.358s

    cat fb.danRer10.chainGalGal6Link.txt
    #	80410462 bases of 1369683683 (5.871%) in intersection
    cat fb.danRer10.chainSynGalGal6Link.txt
    #   17599825 bases of 1369683683 (1.285%) in intersection

    time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \
          danRer10 galGal6) > rbest.log 2>&1
    # real    188m48.335s

    cat fb.danRer10.chainRBest.GalGal6.txt
    #	55546117 bases of 1369683683 (4.055%) in intersection

##############################################################################
# LASTZ Gallus gallus chicken (matHap) GCF_016699485.2 vs. galGal6
#	(DONE - 2021-10-14 - hiram)

    cd /cluster/home/hiram/kent/src/hg/makeDb/doc/galGal6

    time (~/kent/src/hg/utils/automation/pairLastz.sh galGal6 \
      GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b \
         other other) > galGal6.GCF_016699485.2.log 2>&1 &

    #	real	408m10.031s
    #	user	0m1.547s
    #	sys	0m1.169s

    # the following make doc is in that log file, copied here:

##############################################################################
# LASTZ Chicken GalGal6 vs. chicken GCF_016699485.2 (DONE - 2021-10-14 - hiram)
    mkdir /hive/data/genomes/galGal6/bed/lastzGCF_016699485.2.2021-10-14
    cd /hive/data/genomes/galGal6/bed/lastzGCF_016699485.2.2021-10-14

    printf '# chicken GCF_016699485.2 vs. Chicken GalGal6
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz

# TARGET: Chicken GalGal6
SEQ1_DIR=/hive/data/genomes/galGal6/galGal6.2bit
SEQ1_LEN=/hive/data/genomes/galGal6/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
SEQ1_LIMIT=40

# QUERY: chicken GCF_016699485.2
SEQ2_DIR=/hive/data/genomes/asmHubs/GCF/016/699/485/GCF_016699485.2/GCF_016699485.2.2bit
SEQ2_LEN=/hive/data/genomes/asmHubs/GCF/016/699/485/GCF_016699485.2/GCF_016699485.2.chrom.sizes.txt
SEQ2_CHUNK=20000000
SEQ2_LAP=0
SEQ2_LIMIT=100

BASE=/hive/data/genomes/galGal6/bed/lastzGCF_016699485.2.2021-10-14
TMPDIR=/dev/shm

' > DEF

    time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \
       -qAsmId GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
        -chainMinScore=5000 -chainLinearGap=loose) > do.log 2>&1
    grep -w real do.log | sed -e 's/^/    # /;'
    # real	267m30.440s

    sed -e 's/^/    # /;' fb.galGal6.chainGCF_016699485.2Link.txt
    # 1038112746 bases of 1065365425 (97.442%) in intersection
    sed -e 's/^/    # /;' fb.galGal6.chainSynGCF_016699485.2Link.txt
    # 1024082754 bases of 1065365425 (96.125%) in intersection

    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
       \
      -query2Bit="/hive/data/genomes/asmHubs/GCF/016/699/485/GCF_016699485.2/GCF_016699485.2.2bit" \
-querySizes="/hive/data/genomes/asmHubs/GCF/016/699/485/GCF_016699485.2/GCF_016699485.2.chrom.sizes.txt" \
        galGal6 GCF_016699485.2) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	32m59.747s

    sed -e 's/^/    # /;' fb.galGal6.chainRBest.GCF_016699485.2.txt
    # 1017174748 bases of 1065365425 (95.477%) in intersection

    ### and for the swap

    cd /hive/data/genomes/asmHubs/allBuild/GCF/016/699/485/GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b/trackData/blastz.galGal6.swap

   time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \
   -qAsmId GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b /hive/data/genomes/galGal6/bed/lastzGCF_016699485.2.2021-10-14/DEF -swapDir=`pwd` \
  -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
    -chainMinScore=5000 -chainLinearGap=loose) > swap.log 2>&1

    grep -w real swap.log | sed -e 's/^/    # /;'
    # real	74m58.936s

    sed -e 's/^/    # /;' fb.GCF_016699485.2.chainGalGal6Link.txt
    # 1037750321 bases of 1053332251 (98.521%) in intersection
    sed -e 's/^/    # /;' fb.GCF_016699485.2.chainSynGalGal6Link.txt
    # 1023011548 bases of 1053332251 (97.121%) in intersection
\    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
    \
   -target2bit="/hive/data/genomes/asmHubs/GCF/016/699/485/GCF_016699485.2/GCF_016699485.2.2bit" \
-targetSizes="/hive/data/genomes/asmHubs/GCF/016/699/485/GCF_016699485.2/GCF_016699485.2.chrom.sizes.txt" \
   GCF_016699485.2 galGal6) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	32m40.423s

    sed -e 's/^/    # /;' fb.GCF_016699485.2.chainRBest.GalGal6.txt
    # 1017361581 bases of 1053332251 (96.585%) in intersection

##############################################################################
# LASTZ Chicken GalGal6 vs. Ferret MusFur1
#    (DONE - 2025-06-16 - Gerardo)

    mkdir /hive/data/genomes/galGal6/bed/lastzMusFur1.2025-06-16
    cd /hive/data/genomes/galGal6/bed/lastzMusFur1.2025-06-16

    printf '# Ferret MusFur1 vs. Chicken GalGal6
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz

# TARGET: Chicken  galGal6
SEQ1_DIR=/hive/data/genomes/galGal6/galGal6.2bit
SEQ1_LEN=/hive/data/genomes/galGal6/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
SEQ1_LIMIT=40

# QUERY: Ferret  musFur1
SEQ2_DIR=/hive/data/genomes/musFur1/musFur1.2bit
SEQ2_LEN=/hive/data/genomes/musFur1/chrom.sizes
SEQ2_CHUNK=20000000
SEQ2_LAP=0
SEQ2_LIMIT=100

BASE=/hive/data/genomes/galGal6/bed/lastzMusFur1.2025-06-16
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	211m51.107s

    sed -e 's/^/    # /;' fb.galGal6.chainMusFur1Link.txt
    # 65632006 bases of 1055588482 (6.218%) in intersection
    sed -e 's/^/    # /;' fb.galGal6.chainSynMusFur1Link.txt
    # 56367160 bases of 1055588482 (5.340%) in intersection

    time (~/kent/src/hg/utils/automation/doRecipBest.pl  -load -workhorse=hgwdev -buildDir=`pwd` \
       \
       \
        galGal6 musFur1) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	15m23.187s

    sed -e 's/^/    # /;' fb.galGal6.chainRBest.MusFur1.txt
    # 61859234 bases of 1055588482 (5.860%) in intersection

    ### and for the swap

    cd /hive/data/genomes/musFur1/bed/blastz.galGal6.swap

   time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl  -swap -verbose=2 \
    /hive/data/genomes/galGal6/bed/lastzMusFur1.2025-06-16/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	4m33.592s

    sed -e 's/^/    # /;' fb.musFur1.chainGalGal6Link.txt
    # 70918404 bases of 2277906570 (3.113%) in intersection
    sed -e 's/^/    # /;' fb.musFur1.chainSynGalGal6Link.txt
    # 56401202 bases of 2277906570 (2.476%) in intersection
\    time (~/kent/src/hg/utils/automation/doRecipBest.pl  -load -workhorse=hgwdev -buildDir=`pwd` \
    \
    \
   musFur1 galGal6) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	17m4.241s

    sed -e 's/^/    # /;' fb.musFur1.chainRBest.GalGal6.txt
    # 61922846 bases of 2277906570 (2.718%) in intersection

real	248m52.641s
user	0m1.043s
sys	0m0.649s
##############################################################################
