# for emacs: -*- mode: sh; -*-

#########################################################################
# LASTZ human/hg38 bonobo/panPan1 - (DONE - 2014-12-11 - Hiram)
    mkdir /hive/data/genomes/hg38/bed/lastzPanPan1.2014-12-11
    cd /hive/data/genomes/hg38/bed/lastzPanPan1.2014-12-11

    cat << '_EOF_' > DEF
# human vs bonobo
# parameters obtained from a tuning run of lastz_D
# /hive/users/hiram/multiz/100way/hg38.panPan1/hg38.panPan1.tuning.top400.txt

BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.54/bin/lastz
BLASTZ_T=2
BLASTZ_O=400
BLASTZ_E=30
BLASTZ_M=254
BLASTZ_X=1000
BLASTZ_Y=3400
BLASTZ_Q=/hive/data/genomes/hg38/bed/lastzPanPan1.2014-12-11/hg38.panPan1.tuning.Q.txt
#       A     C     G     T
# A   100  -174   -43  -143
# C  -174    91  -179   -43
# G   -43  -179    91  -174
# T  -143   -43  -174   100

# TARGET: human hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CTGDIR=/hive/data/genomes/hg38/hg38.contigs.2bit
SEQ1_CTGLEN=/hive/data/genomes/hg38/hg38.contigs.chrom.sizes
SEQ1_LIFT=/hive/data/genomes/hg38/jkStuff/hg38.contigs.lift
SEQ1_CHUNK=40000000
SEQ1_LIMIT=10
SEQ1_LAP=10000

# QUERY: bonobo panPan1
SEQ2_DIR=/hive/data/genomes/panPan1/panPan1.2bit
SEQ2_LEN=/hive/data/genomes/panPan1/chrom.sizes
SEQ2_CHUNK=20000000
SEQ2_LIMIT=50
SEQ2_LAP=0

BASE=/hive/data/genomes/hg38/bed/lastzPanPan1.2014-12-11
TMPDIR=/dev/shm
'_EOF_'
    # << happy emacs

    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
        -chainMinScore=3000 -chainLinearGap=medium \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > do.log 2>&1
    # real    197m51.411s

    cat fb.hg38.chainPanPan1Link.txt
    # 2833718712 bases of 3049335806 (92.929%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` hg38 panPan1) > rbest.log 2>&1 &
    # real    44m15.208s

    # and for the swap:
    mkdir /hive/data/genomes/panPan1/bed/blastz.hg38.swap
    cd /hive/data/genomes/panPan1/bed/blastz.hg38.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/hg38/bed/lastzPanPan1.2014-12-11/DEF \
        -swap -chainMinScore=3000 -chainLinearGap=medium \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    #  real    117m56.319s

    cat fb.panPan1.chainHg38Link.txt
    # 2665801248 bases of 2725905606 (97.795%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` panPan1 hg38) > rbest.log 2>&1
    # real    79m30.931s

#########################################################################
# LASTZ human/hg38 Golden snub-nosed monkey/rhiRox1 - (DONE - 2015-02-23 - Hiram)
    mkdir /hive/data/genomes/hg38/bed/lastzRhiRox1.2015-02-23
    cd /hive/data/genomes/hg38/bed/lastzRhiRox1.2015-02-23

    cp -p \
/hive/users/hiram/multiz/100way/hg38.rhiRox1/hg38.rhiRox1.tuning.top300.txt \
     ./hg38.rhiRox1.tuning.Q.txt

    cat << '_EOF_' > DEF
# human vs Golden snub-nosed monkey
# parameters obtained from a tuning run of lastz_D
# /hive/users/hiram/multiz/100way/hg38.rhiRox1/hg38.rhiRox1.tuning.top300.txt

BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.54/bin/lastz
BLASTZ_T=2
BLASTZ_O=400
BLASTZ_E=30
BLASTZ_M=254
BLASTZ_X=1000
BLASTZ_Y=3400
BLASTZ_Q=/hive/data/genomes/hg38/bed/lastzRhiRox1.2015-02-23/hg38.rhiRox1.tuning.Q.txt
#       A     C     G     T
# A   100  -176   -44  -147
# C  -176    93  -178   -44
# G   -44  -178    93  -176
# T  -147   -44  -176   100

# TARGET: human hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CTGDIR=/hive/data/genomes/hg38/hg38.contigs.2bit
SEQ1_CTGLEN=/hive/data/genomes/hg38/hg38.contigs.chrom.sizes
SEQ1_LIFT=/hive/data/genomes/hg38/jkStuff/hg38.contigs.lift
SEQ1_CHUNK=40000000
SEQ1_LIMIT=10
SEQ1_LAP=10000

# QUERY: Golden snub-nosed monkey rhiRox1
SEQ2_DIR=/hive/data/genomes/rhiRox1/rhiRox1.2bit
SEQ2_LEN=/hive/data/genomes/rhiRox1/chrom.sizes
SEQ2_CHUNK=20000000
SEQ2_LIMIT=300
SEQ2_LAP=0

BASE=/hive/data/genomes/hg38/bed/lastzRhiRox1.2015-02-23
TMPDIR=/dev/shm
'_EOF_'
    # << happy emacs

    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
        -chainMinScore=3000 -chainLinearGap=medium \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > do.log 2>&1
    # real    218m48.221s

    cat fb.hg38.chainRhiRox1Link.txt
    # 2595256243 bases of 3049335806 (85.109%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` hg38 rhiRox1) \
       > rbest.log 2>&1 &
    # real    53m54.908s
    time (doRecipBest.pl -load -continue=load -workhorse=hgwdev \
	-buildDir=`pwd` hg38 rhiRox1) > loadRBest.log 2>&1 &
    cat fb.hg38.chainRBestRhiRox1Link.txt
    # 2400873699 bases of 3049335806 (78.734%) in intersection

    # create and load up syntenic chainNet: 2017-10-27
cd /hive/data/genomes/hg38/bed/lastzRhiRox1.2015-02-23/axtChain
netToAxt hg38.rhiRox1.syn.net.gz hg38.rhiRox1.all.chain.gz \
/scratch/data/hg38/hg38.2bit /hive/data/genomes/rhiRox1/rhiRox1.2bit stdout \
  | axtSort stdin stdout \
     | axtToChain stdin /hive/data/genomes/hg38/chrom.sizes \
        /hive/data/genomes/rhiRox1/chrom.sizes stdout \
            | gzip -c > hg38.rhiRox1.syn.chain.gz
hgLoadChain -tIndex hg38 chainSynRhiRox1 hg38.rhiRox1.syn.chain.gz
netFilter -minGap=10 hg38.rhiRox1.syn.net.gz \
  | hgLoadNet -verbose=0 hg38 netSynRhiRox1 stdin
cd /hive/data/genomes/hg38/bed/lastzRhiRox1.2015-02-23
featureBits hg38 chainSynRhiRox1Link > fb.hg38.chainSynRhiRox1Link.txt 2>&1
cat fb.hg38.chainSynRhiRox1Link.txt
    # 2538430248 bases of 3049335806 (83.245%) in intersection

    # and for the swap:
    mkdir /hive/data/genomes/rhiRox1/bed/blastz.hg38.swap
    cd /hive/data/genomes/rhiRox1/bed/blastz.hg38.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/hg38/bed/lastzRhiRox1.2015-02-23/DEF \
        -swap -chainMinScore=3000 -chainLinearGap=medium \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    #  real    174m27.934s

    cat fb.rhiRox1.chainHg38Link.txt
    # 2474156996 bases of 2856044136 (86.629%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` rhiRox1 hg38) \
       > rbest.log 2>&1
    # real    83m2.776s

#########################################################################
# LASTZ human/hg38 Gibbon/nomLeu3 - (DONE - 2014-12-12 - Hiram)
    mkdir /hive/data/genomes/hg38/bed/lastzNomLeu3.2014-12-12
    cd /hive/data/genomes/hg38/bed/lastzNomLeu3.2014-12-12

    cp -p \
/hive/users/hiram/multiz/100way/hg38.nomLeu3/hg38.nomLeu3.tuning.top200.txt \
     ./hg38.nomLeu3.tuning.Q.txt

    cat << '_EOF_' > DEF
# human vs Gibbon
# parameters obtained from a tuning run of lastz_D
# /hive/users/hiram/multiz/100way/hg38.nomLeu3/hg38.nomLeu3.tuning.top200.txt
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.54/bin/lastz
BLASTZ_T=2
BLASTZ_O=400
BLASTZ_E=30
BLASTZ_M=254
BLASTZ_X=1000
BLASTZ_Y=3400
BLASTZ_Q=/hive/data/genomes/hg38/bed/lastzNomLeu3.2014-12-12/hg38.nomLeu3.tuning.Q.txt
#       A     C     G     T
# A   100  -175   -43  -144
# C  -175    92  -180   -43
# G   -43  -180    92  -175
# T  -144   -43  -175   100

# TARGET: human hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CTGDIR=/hive/data/genomes/hg38/hg38.contigs.2bit
SEQ1_CTGLEN=/hive/data/genomes/hg38/hg38.contigs.chrom.sizes
SEQ1_LIFT=/hive/data/genomes/hg38/jkStuff/hg38.contigs.lift
SEQ1_CHUNK=40000000
SEQ1_LIMIT=10
SEQ1_LAP=10000

# QUERY: Gibbon nomLeu3
SEQ2_DIR=/hive/data/genomes/nomLeu3/nomLeu3.2bit
SEQ2_LEN=/hive/data/genomes/nomLeu3/chrom.sizes
SEQ2_CHUNK=20000000
SEQ2_LIMIT=50
SEQ2_LAP=0

BASE=/hive/data/genomes/hg38/bed/lastzNomLeu3.2014-12-12
TMPDIR=/dev/shm
'_EOF_'
    # << happy emacs

    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
        -chainMinScore=3000 -chainLinearGap=medium \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > do.log 2>&1
    # real    366m25.258s

    cat fb.hg38.chainNomLeu3Link.txt
    # 2633978949 bases of 3049335806 (86.379%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` hg38 nomLeu3) > rbest.log 2>&1 &
    # real    77m44.300s
    time (doRecipBest.pl -load -continue=load -workhorse=hgwdev \
	-buildDir=`pwd` hg38 nomLeu3) > loadRBest.log 2>&1 &
    cat fb.hg38.chainRBestNomLeu3Link.txt
    # 2442160816 bases of 3049335806 (80.088%) in intersection

    # create and load up syntenic chainNet: 2017-10-27
cd /hive/data/genomes/hg38/bed/lastzNomLeu3.2014-12-12/axtChain
netToAxt hg38.nomLeu3.syn.net.gz hg38.nomLeu3.all.chain.gz \
/scratch/data/hg38/hg38.2bit /hive/data/genomes/nomLeu3/nomLeu3.2bit stdout \
  | axtSort stdin stdout \
     | axtToChain stdin /hive/data/genomes/hg38/chrom.sizes \
        /hive/data/genomes/nomLeu3/chrom.sizes stdout \
            | gzip -c > hg38.nomLeu3.syn.chain.gz
hgLoadChain -tIndex hg38 chainSynNomLeu3 hg38.nomLeu3.syn.chain.gz
netFilter -minGap=10 hg38.nomLeu3.syn.net.gz \
  | hgLoadNet -verbose=0 hg38 netSynNomLeu3 stdin
cd /hive/data/genomes/hg38/bed/lastzNomLeu3.2014-12-12
featureBits hg38 chainSynNomLeu3Link > fb.hg38.chainSynNomLeu3Link.txt 2>&1
cat fb.hg38.chainSynNomLeu3Link.txt
    2577846437 bases of 3049335806 (84.538%) in intersection

    real    7m3.732s

    # and for the swap:
    mkdir /hive/data/genomes/nomLeu3/bed/blastz.hg38.swap
    cd /hive/data/genomes/nomLeu3/bed/blastz.hg38.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/hg38/bed/lastzNomLeu3.2014-12-12/DEF \
        -swap -chainMinScore=3000 -chainLinearGap=medium \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    #  real    120m35.210s

    cat fb.nomLeu3.chainHg38Link.txt
    # 2493897222 bases of 2756609047 (90.470%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` nomLeu3 hg38) > rbest.log 2>&1
    # real    39m37.872s

#########################################################################
# LASTZ human/hg38 Squirrel monkey/saiBol1 - (DONE - 2014-12-13 - Hiram)
    mkdir /hive/data/genomes/hg38/bed/lastzSaiBol1.2014-12-13
    cd /hive/data/genomes/hg38/bed/lastzSaiBol1.2014-12-13

    cp -p \
/hive/users/hiram/multiz/100way/hg38.saiBol1/hg38.saiBol1.tuning.top300.txt \
     ./hg38.saiBol1.tuning.Q.txt

    cat << '_EOF_' > DEF
# human vs Squirrel monkey
# parameters obtained from a tuning run of lastz_D
# /hive/users/hiram/multiz/100way/hg38.saiBol1/hg38.saiBol1.tuning.top300.txt
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.54/bin/lastz
BLASTZ_T=2
BLASTZ_O=400
BLASTZ_E=30
BLASTZ_M=254
BLASTZ_X=1000
BLASTZ_Y=3400
BLASTZ_Q=/hive/data/genomes/hg38/bed/lastzSaiBol1.2014-12-13/hg38.saiBol1.tuning.Q.txt
#       A     C     G     T
# A   100  -178   -40  -145
# C  -178    93  -188   -40
# G   -40  -188    93  -178
# T  -145   -40  -178   100

# TARGET: human hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CTGDIR=/hive/data/genomes/hg38/hg38.contigs.2bit
SEQ1_CTGLEN=/hive/data/genomes/hg38/hg38.contigs.chrom.sizes
SEQ1_LIFT=/hive/data/genomes/hg38/jkStuff/hg38.contigs.lift
SEQ1_CHUNK=40000000
SEQ1_LIMIT=10
SEQ1_LAP=10000

# QUERY: Squirrel monkey saiBol1
SEQ2_DIR=/hive/data/genomes/saiBol1/saiBol1.2bit
SEQ2_LEN=/hive/data/genomes/saiBol1/chrom.sizes
SEQ2_CHUNK=20000000
SEQ2_LIMIT=20
SEQ2_LAP=0

BASE=/hive/data/genomes/hg38/bed/lastzSaiBol1.2014-12-13
TMPDIR=/dev/shm
'_EOF_'
    # << happy emacs

    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
        -chainMinScore=3000 -chainLinearGap=medium \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > do.log 2>&1
    # real    321m56.693s

    cat fb.hg38.chainSaiBol1Link.txt
    # 2151771087 bases of 3049335806 (70.565%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` hg38 saiBol1) > rbest.log 2>&1 &
    # real    129m56.144s
    time (doRecipBest.pl -load -continue=load -workhorse=hgwdev \
	-buildDir=`pwd` hg38 saiBol1) > loadRBest.log 2>&1 &
    cat fb.hg38.chainRBestSaiBol1Link.txt
    # 1986661464 bases of 3049335806 (65.151%) in intersection

    # create and load up syntenic chainNet: 2017-10-27
cd /hive/data/genomes/hg38/bed/lastzSaiBol1.2014-12-13/axtChain
netToAxt hg38.saiBol1.syn.net.gz hg38.saiBol1.all.chain.gz \
/scratch/data/hg38/hg38.2bit /hive/data/genomes/saiBol1/saiBol1.2bit stdout \
  | axtSort stdin stdout \
     | axtToChain stdin /hive/data/genomes/hg38/chrom.sizes \
        /hive/data/genomes/saiBol1/chrom.sizes stdout \
            | gzip -c > hg38.saiBol1.syn.chain.gz
hgLoadChain -tIndex hg38 chainSynSaiBol1 hg38.saiBol1.syn.chain.gz
netFilter -minGap=10 hg38.saiBol1.syn.net.gz \
  | hgLoadNet -verbose=0 hg38 netSynSaiBol1 stdin
cd /hive/data/genomes/hg38/bed/lastzSaiBol1.2014-12-13
featureBits hg38 chainSynSaiBol1Link > fb.hg38.chainSynSaiBol1Link.txt 2>&1
cat fb.hg38.chainSynSaiBol1Link.txt
    # 2096151749 bases of 3049335806 (68.741%) in intersection

    # real    10m12.757s

    # and for the swap:
    mkdir /hive/data/genomes/saiBol1/bed/blastz.hg38.swap
    cd /hive/data/genomes/saiBol1/bed/blastz.hg38.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/hg38/bed/lastzSaiBol1.2014-12-13/DEF \
        -swap -chainMinScore=3000 -chainLinearGap=medium \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    #  real    102m22.969s

    cat fb.saiBol1.chainHg38Link.txt
    # 2018022119 bases of 2477131095 (81.466%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` saiBol1 hg38) > rbest.log 2>&1
    # real    42m24.226s

#########################################################################
# LASTZ human/hg38 Crab-eating macaque/macFas5 - (DONE - 2014-12-13 - Hiram)
    mkdir /hive/data/genomes/hg38/bed/lastzMacFas5.2014-12-13
    cd /hive/data/genomes/hg38/bed/lastzMacFas5.2014-12-13

    cp -p \
/hive/users/hiram/multiz/100way/hg38.macFas5/hg38.macFas5.tuning.top300.txt \
     ./hg38.macFas5.tuning.Q.txt

    cat << '_EOF_' > DEF
# human vs Crab-eating macaque
# parameters obtained from a tuning run of lastz_D
# /hive/users/hiram/multiz/100way/hg38.macFas5/hg38.macFas5.tuning.top300.txt
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.54/bin/lastz
BLASTZ_T=2
BLASTZ_O=400
BLASTZ_E=30
BLASTZ_M=254
BLASTZ_X=1000
BLASTZ_Y=3400
BLASTZ_Q=/hive/data/genomes/hg38/bed/lastzMacFas5.2014-12-13/hg38.macFas5.tuning.Q.txt
#       A     C     G     T
# A   100  -174   -43  -144
# C  -174    93  -176   -43
# G   -43  -176    93  -174
# T  -144   -43  -174   100

# TARGET: human hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CTGDIR=/hive/data/genomes/hg38/hg38.contigs.2bit
SEQ1_CTGLEN=/hive/data/genomes/hg38/hg38.contigs.chrom.sizes
SEQ1_LIFT=/hive/data/genomes/hg38/jkStuff/hg38.contigs.lift
SEQ1_CHUNK=40000000
SEQ1_LIMIT=10
SEQ1_LAP=10000

# QUERY: Crab-eating macaque macFas5
SEQ2_DIR=/hive/data/genomes/macFas5/macFas5.2bit
SEQ2_LEN=/hive/data/genomes/macFas5/chrom.sizes
SEQ2_CHUNK=20000000
SEQ2_LIMIT=20
SEQ2_LAP=0

BASE=/hive/data/genomes/hg38/bed/lastzMacFas5.2014-12-13
TMPDIR=/dev/shm
'_EOF_'
    # << happy emacs

    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
        -chainMinScore=3000 -chainLinearGap=medium \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > do.log 2>&1
    # real    669m24.572s

    cat fb.hg38.chainMacFas5Link.txt
    # 2612527708 bases of 3049335806 (85.675%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` hg38 macFas5) > rbest.log 2>&1 &
    # real    47m25.375s
    time (doRecipBest.pl -load -continue=load -workhorse=hgwdev \
	-buildDir=`pwd` hg38 macFas5) > loadRBest.log 2>&1 &
    cat fb.hg38.chainRBestMacFas5Link.txt
    # 2423088291 bases of 3049335806 (79.463%) in intersection

    # create and load up syntenic chainNet: 2017-10-27
cd /hive/data/genomes/hg38/bed/lastzMacFas5.2014-12-13/axtChain
netToAxt hg38.macFas5.syn.net.gz hg38.macFas5.all.chain.gz \
/scratch/data/hg38/hg38.2bit /hive/data/genomes/macFas5/macFas5.2bit stdout \
  | axtSort stdin stdout \
     | axtToChain stdin /hive/data/genomes/hg38/chrom.sizes \
        /hive/data/genomes/macFas5/chrom.sizes stdout \
            | gzip -c > hg38.macFas5.syn.chain.gz
hgLoadChain -tIndex hg38 chainSynMacFas5 hg38.macFas5.syn.chain.gz
netFilter -minGap=10 hg38.macFas5.syn.net.gz \
  | hgLoadNet -verbose=0 hg38 netSynMacFas5 stdin
cd /hive/data/genomes/hg38/bed/lastzMacFas5.2014-12-13
featureBits hg38 chainSynMacFas5Link > fb.hg38.chainSynMacFas5Link.txt 2>&1
cat fb.hg38.chainSynMacFas5Link.txt
# 2557788563 bases of 3049335806 (83.880%) in intersection

    # and for the swap:
    mkdir /hive/data/genomes/macFas5/bed/blastz.hg38.swap
    cd /hive/data/genomes/macFas5/bed/blastz.hg38.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/hg38/bed/lastzMacFas5.2014-12-13/DEF \
        -swap -chainMinScore=3000 -chainLinearGap=medium \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    #  real    120m29.355s

    cat fb.macFas5.chainHg38Link.txt
    # 2460372459 bases of 2803866698 (87.749%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` macFas5 hg38) > rbest.log 2>&1
    # real    66m23.284s

#########################################################################
# LASTZ human/hg38 Bushbaby/otoGar3 - (DONE - 2015-02-22 - Hiram)
    mkdir /hive/data/genomes/hg38/bed/lastzOtoGar3.2015-02-22
    cd /hive/data/genomes/hg38/bed/lastzOtoGar3.2015-02-22

    cat << '_EOF_' > DEF
# human vs Bushbaby
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz
BLASTZ_T=2
BLASTZ_O=400
BLASTZ_E=30
BLASTZ_M=254
# default BLASTZ_Q score matrix:
#       A     C     G     T
# A    91  -114   -31  -123
# C  -114   100  -125   -31
# G   -31  -125   100  -114
# T  -123   -31  -114    91

# TARGET: human hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CTGDIR=/hive/data/genomes/hg38/hg38.contigs.2bit
SEQ1_CTGLEN=/hive/data/genomes/hg38/hg38.contigs.chrom.sizes
SEQ1_LIFT=/hive/data/genomes/hg38/jkStuff/hg38.contigs.lift
SEQ1_CHUNK=40000000
SEQ1_LIMIT=10
SEQ1_LAP=10000

# QUERY: Bushbaby otoGar3
SEQ2_DIR=/hive/data/genomes/otoGar3/otoGar3.2bit
SEQ2_LEN=/hive/data/genomes/otoGar3/chrom.sizes
SEQ2_CHUNK=20000000
SEQ2_LIMIT=20
SEQ2_LAP=0

BASE=/hive/data/genomes/hg38/bed/lastzOtoGar3.2015-02-22
TMPDIR=/dev/shm
'_EOF_'
    # << happy emacs

    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
        -chainMinScore=3000 -chainLinearGap=medium \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > do.log 2>&1
    # real    336m10.091s

    cat fb.hg38.chainOtoGar3Link.txt
    # 1622122468 bases of 3049335806 (53.196%) in intersection
    # replacing previous tuned version:
    # 1508964214 bases of 3049335806 (49.485%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` hg38 otoGar3) \
       > rbest.log 2>&1 &
    # real    59m25.363s
    # mistakenly destroyed the rbest.log file:
    time (doRecipBest.pl -load -continue=load -workhorse=hgwdev \
	-buildDir=`pwd` hg38 otoGar3) > rbest.log 2>&1 &
    # real    13m9.418s

    cat fb.hg38.chainRBestOtoGar3Link.txt
    # 1482204777 bases of 3049335806 (48.607%) in intersection

    # create and load up syntenic chainNet: 2017-10-27
cd /hive/data/genomes/hg38/bed/lastzOtoGar3.2015-02-22/axtChain
netToAxt hg38.otoGar3.syn.net.gz hg38.otoGar3.all.chain.gz \
/scratch/data/hg38/hg38.2bit /hive/data/genomes/otoGar3/otoGar3.2bit stdout \
  | axtSort stdin stdout \
     | axtToChain stdin /hive/data/genomes/hg38/chrom.sizes \
        /hive/data/genomes/otoGar3/chrom.sizes stdout \
            | gzip -c > hg38.otoGar3.syn.chain.gz
hgLoadChain -tIndex hg38 chainSynOtoGar3 hg38.otoGar3.syn.chain.gz
netFilter -minGap=10 hg38.otoGar3.syn.net.gz \
  | hgLoadNet -verbose=0 hg38 netSynOtoGar3 stdin
cd /hive/data/genomes/hg38/bed/lastzOtoGar3.2015-02-22
featureBits hg38 chainSynOtoGar3Link > fb.hg38.chainSynOtoGar3Link.txt 2>&1
cat fb.hg38.chainSynOtoGar3Link.txt
# 1547295352 bases of 3049335806 (50.742%) in intersection

    # and for the swap:
    mkdir /hive/data/genomes/otoGar3/bed/blastz.hg38.swap
    cd /hive/data/genomes/otoGar3/bed/blastz.hg38.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/hg38/bed/lastzOtoGar3.2015-02-22/DEF \
        -swap -chainMinScore=3000 -chainLinearGap=medium \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    #  real    115m47.941s

    cat fb.otoGar3.chainHg38Link.txt
    # 1531320942 bases of 2359530453 (64.899%) in intersection
    # replacing previous tuned version:
    # 1428944740 bases of 2359530453 (60.561%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` otoGar3 hg38) > rbest.log 2>&1
    # real    46m56.972s

#########################################################################
# LASTZ human/hg38 Marmoset/calJac3 - (DONE - 2014-12-13 - Hiram)
    mkdir /hive/data/genomes/hg38/bed/lastzCalJac3.2014-12-13
    cd /hive/data/genomes/hg38/bed/lastzCalJac3.2014-12-13

    cp -p \
/hive/users/hiram/multiz/100way/hg38.calJac3/hg38.calJac3.tuning.top300.txt \
     ./hg38.calJac3.tuning.Q.txt

    cat << '_EOF_' > DEF
# human vs Marmoset
# parameters obtained from a tuning run of lastz_D
# /hive/users/hiram/multiz/100way/hg38.calJac3/hg38.calJac3.tuning.top300.txt

BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.54/bin/lastz
BLASTZ_T=2
BLASTZ_O=400
BLASTZ_E=30
BLASTZ_M=254
BLASTZ_X=1000
BLASTZ_Y=3400
BLASTZ_Q=/hive/data/genomes/hg38/bed/lastzCalJac3.2014-12-13/hg38.calJac3.tuning.Q.txt
#       A     C     G     T
# A   100  -176   -40  -145
# C  -176    94  -186   -40
# G   -40  -186    94  -176
# T  -145   -40  -176   100

# TARGET: human hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CTGDIR=/hive/data/genomes/hg38/hg38.contigs.2bit
SEQ1_CTGLEN=/hive/data/genomes/hg38/hg38.contigs.chrom.sizes
SEQ1_LIFT=/hive/data/genomes/hg38/jkStuff/hg38.contigs.lift
SEQ1_CHUNK=40000000
SEQ1_LIMIT=10
SEQ1_LAP=10000

# QUERY: Marmoset calJac3
SEQ2_DIR=/hive/data/genomes/calJac3/calJac3.2bit
SEQ2_LEN=/hive/data/genomes/calJac3/chrom.sizes
SEQ2_CHUNK=20000000
SEQ2_LIMIT=40
SEQ2_LAP=0

BASE=/hive/data/genomes/hg38/bed/lastzCalJac3.2014-12-13
TMPDIR=/dev/shm
'_EOF_'
    # << happy emacs

    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
        -chainMinScore=3000 -chainLinearGap=medium \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > do.log 2>&1
    # real    486m51.449s

    cat fb.hg38.chainCalJac3Link.txt
    # 2186651179 bases of 3049335806 (71.709%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` hg38 calJac3) > rbest.log 2>&1 &
    # real    50m52.928s
    time (doRecipBest.pl -load -continue=load -workhorse=hgwdev \
	-buildDir=`pwd` hg38 calJac3) > loadRBest.log 2>&1 &
    cat fb.hg38.chainRBestCalJac3Link.txt
    # 2019861688 bases of 3049335806 (66.239%) in intersection

    # create and load up syntenic chainNet: 2017-10-27
cd /hive/data/genomes/hg38/bed/lastzCalJac3.2014-12-13
netToAxt hg38.calJac3.syn.net.gz hg38.calJac3.all.chain.gz \
/scratch/data/hg38/hg38.2bit /hive/data/genomes/calJac3/calJac3.2bit stdout \
  | axtSort stdin stdout \
     | axtToChain stdin /hive/data/genomes/hg38/chrom.sizes \
        /hive/data/genomes/calJac3/chrom.sizes stdout \
            | gzip -c > hg38.calJac3.syn.chain.gz
hgLoadChain -tIndex hg38 chainSynCalJac3 hg38.calJac3.syn.chain.gz
netFilter -minGap=10 hg38.calJac3.syn.net.gz \
  | hgLoadNet -verbose=0 hg38 netSynCalJac3 stdin
cd /hive/data/genomes/hg38/bed/lastzCalJac3.2014-12-13
featureBits hg38 chainSynCalJac3Link > fb.hg38.chainSynCalJac3Link.txt 2>&1
cat fb.hg38.chainSynCalJac3Link.txt
# 2119273306 bases of 3049335806 (69.500%) in intersection

    # and for the swap:
    mkdir /hive/data/genomes/calJac3/bed/blastz.hg38.swap
    cd /hive/data/genomes/calJac3/bed/blastz.hg38.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/hg38/bed/lastzCalJac3.2014-12-13/DEF \
        -swap -chainMinScore=3000 -chainLinearGap=medium \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    #  real    125m9.577s

    cat fb.calJac3.chainHg38Link.txt
    # 2112735553 bases of 2752505800 (76.757%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` calJac3 hg38) > rbest.log 2>&1

#########################################################################
# LASTZ human/hg38 Gorilla/gorGor3 - (DONE - 2014-12-13 - Hiram)
    mkdir /hive/data/genomes/hg38/bed/lastzGorGor3.2014-12-13
    cd /hive/data/genomes/hg38/bed/lastzGorGor3.2014-12-13

    cat << '_EOF_' > DEF
# human vs Gorilla
# parameters obtained from a tuning run of lastz_D
# /hive/users/hiram/multiz/100way/hg38.gorGor3/hg38.gorGor3.tuning.top200.txt

BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.54/bin/lastz
BLASTZ_T=2
BLASTZ_O=400
BLASTZ_E=30
BLASTZ_M=254
BLASTZ_X=1000
BLASTZ_Y=3400
BLASTZ_Q=/hive/data/genomes/hg38/bed/lastzGorGor3.2014-12-13/hg38.gorGor3.tuning.Q.txt
#       A     C     G     T
# A   100  -177   -41  -144
# C  -177    93  -184   -41
# G   -41  -184    93  -177
# T  -144   -41  -177   100

# TARGET: human hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CTGDIR=/hive/data/genomes/hg38/hg38.contigs.2bit
SEQ1_CTGLEN=/hive/data/genomes/hg38/hg38.contigs.chrom.sizes
SEQ1_LIFT=/hive/data/genomes/hg38/jkStuff/hg38.contigs.lift
SEQ1_CHUNK=40000000
SEQ1_LIMIT=10
SEQ1_LAP=10000

# QUERY: Gorilla gorGor3
SEQ2_DIR=/hive/data/genomes/gorGor3/gorGor3.2bit
SEQ2_LEN=/hive/data/genomes/gorGor3/chrom.sizes
SEQ2_CHUNK=20000000
SEQ2_LIMIT=100
SEQ2_LAP=0

BASE=/hive/data/genomes/hg38/bed/lastzGorGor3.2014-12-13
TMPDIR=/dev/shm
'_EOF_'
    # << happy emacs

    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
        -chainMinScore=3000 -chainLinearGap=medium \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > do.log 2>&1
    # real    2846m38.709s

    cat fb.hg38.chainGorGor3Link.txt
    # 2683571923 bases of 3049335806 (88.005%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` hg38 gorGor3) > rbest.log 2>&1 &
    # real    42m25.526s

    # and for the swap:
    mkdir /hive/data/genomes/gorGor3/bed/blastz.hg38.swap
    cd /hive/data/genomes/gorGor3/bed/blastz.hg38.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/hg38/bed/lastzGorGor3.2014-12-13/DEF \
        -swap -chainMinScore=3000 -chainLinearGap=medium \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    #  real    116m45.998s

    cat fb.gorGor3.chainHg38Link.txt
    # 2588342923 bases of 2822760080 (91.695%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` gorGor3 hg38) > rbest.log 2>&1
    # real    42m41.291s

#########################################################################
# LASTZ human/hg38 Baboon/papAnu2 - (DONE - 2014-12-13 - Hiram)
    mkdir /hive/data/genomes/hg38/bed/lastzPapAnu2.2014-12-13
    cd /hive/data/genomes/hg38/bed/lastzPapAnu2.2014-12-13

    cp -p \
/hive/users/hiram/multiz/100way/hg38.papAnu2/hg38.papAnu2.tuning.top200.txt \
     ./hg38.papAnu2.tuning.Q.txt

    cat << '_EOF_' > DEF
# human vs Baboon
# parameters obtained from a tuning run of lastz_D
# /hive/users/hiram/multiz/100way/hg38.papAnu2/hg38.papAnu2.tuning.top400.txt

BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.54/bin/lastz
BLASTZ_T=2
BLASTZ_O=400
BLASTZ_E=30
BLASTZ_M=254
BLASTZ_X=1000
BLASTZ_Y=3400
BLASTZ_Q=/hive/data/genomes/hg38/bed/lastzPapAnu2.2014-12-13/hg38.papAnu2.tuning.Q.txt
#       A     C     G     T
# A   100  -173   -45  -144
# C  -173    92  -175   -45
# G   -45  -175    92  -173
# T  -144   -45  -173   100

# TARGET: human hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CTGDIR=/hive/data/genomes/hg38/hg38.contigs.2bit
SEQ1_CTGLEN=/hive/data/genomes/hg38/hg38.contigs.chrom.sizes
SEQ1_LIFT=/hive/data/genomes/hg38/jkStuff/hg38.contigs.lift
SEQ1_CHUNK=40000000
SEQ1_LIMIT=10
SEQ1_LAP=10000

# QUERY: Baboon papAnu2
SEQ2_DIR=/hive/data/genomes/papAnu2/papAnu2.2bit
SEQ2_LEN=/hive/data/genomes/papAnu2/chrom.sizes
SEQ2_CHUNK=20000000
SEQ2_LIMIT=200
SEQ2_LAP=0

BASE=/hive/data/genomes/hg38/bed/lastzPapAnu2.2014-12-13
TMPDIR=/dev/shm
'_EOF_'
    # << happy emacs

    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
        -chainMinScore=3000 -chainLinearGap=medium \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > do.log 2>&1
    # real    406m41.281s

    cat fb.hg38.chainPapAnu2Link.txt
    # 2566899753 bases of 3049335806 (84.179%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` hg38 papAnu2) > rbest.log 2>&1 &
    # real    63m38.539s

    # and for the swap:
    mkdir /hive/data/genomes/papAnu2/bed/blastz.hg38.swap
    cd /hive/data/genomes/papAnu2/bed/blastz.hg38.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/hg38/bed/lastzPapAnu2.2014-12-13/DEF \
        -swap -chainMinScore=3000 -chainLinearGap=medium \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    #  real    118m55.487s

    cat fb.papAnu2.chainHg38Link.txt
    # 2444845897 bases of 2893250291 (84.502%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` papAnu2 hg38) > rbest.log 2>&1
    # real    57m47.118s

#########################################################################
# LASTZ human/hg38 Proboscis monkey/nasLar1 - (DONE - 2014-12-15 - Hiram)
    mkdir /hive/data/genomes/hg38/bed/lastzNasLar1.2014-12-15
    cd /hive/data/genomes/hg38/bed/lastzNasLar1.2014-12-15

    cp -p \
/hive/users/hiram/multiz/100way/hg38.nasLar1/hg38.nasLar1.tuning.top300.txt \
     ./hg38.nasLar1.tuning.Q.txt

    cat << '_EOF_' > DEF
# human vs Proboscis monkey
# parameters obtained from a tuning run of lastz_D
# /hive/users/hiram/multiz/100way/hg38.nasLar1/hg38.nasLar1.tuning.top300.txt

BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.54/bin/lastz
BLASTZ_T=2
BLASTZ_O=400
BLASTZ_E=30
BLASTZ_M=254
BLASTZ_X=1000
BLASTZ_Y=3400
BLASTZ_Q=/hive/data/genomes/hg38/bed/lastzNasLar1.2014-12-15/hg38.nasLar1.tuning.Q.txt
#       A     C     G     T
# A   100  -177   -41  -145
# C  -177    94  -181   -41
# G   -41  -181    94  -177
# T  -145   -41  -177   100

# TARGET: human hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CTGDIR=/hive/data/genomes/hg38/hg38.contigs.2bit
SEQ1_CTGLEN=/hive/data/genomes/hg38/hg38.contigs.chrom.sizes
SEQ1_LIFT=/hive/data/genomes/hg38/jkStuff/hg38.contigs.lift
SEQ1_CHUNK=40000000
SEQ1_LIMIT=10
SEQ1_LAP=10000

# QUERY: Proboscis monkey nasLar1
SEQ2_DIR=/hive/data/genomes/nasLar1/nasLar1.2bit
SEQ2_LEN=/hive/data/genomes/nasLar1/chrom.sizes
SEQ2_CHUNK=20000000
SEQ2_LIMIT=700
SEQ2_LAP=0

BASE=/hive/data/genomes/hg38/bed/lastzNasLar1.2014-12-15
TMPDIR=/dev/shm
'_EOF_'
    # << happy emacs

    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
        -chainMinScore=3000 -chainLinearGap=medium \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > do.log 2>&1
    # real    485m32.959s

    cat fb.hg38.chainNasLar1Link.txt
    # 2272993702 bases of 3049335806 (74.541%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` hg38 nasLar1) > rbest.log 2>&1 &
    # real    55m14.954s
    time (doRecipBest.pl -load -continue=load -workhorse=hgwdev \
	-buildDir=`pwd` hg38 nasLar1) > loadRBest.log 2>&1 &
    cat fb.hg38.chainRBestNasLar1Link.txt
    # 2091196276 bases of 3049335806 (68.579%) in intersection

    # create and load up syntenic chainNet: 2017-10-27
cd /hive/data/genomes/hg38/bed/lastzNasLar1.2014-12-15/axtChain
netToAxt hg38.nasLar1.syn.net.gz hg38.nasLar1.all.chain.gz \
/scratch/data/hg38/hg38.2bit /hive/data/genomes/nasLar1/nasLar1.2bit stdout \
  | axtSort stdin stdout \
     | axtToChain stdin /hive/data/genomes/hg38/chrom.sizes \
        /hive/data/genomes/nasLar1/chrom.sizes stdout \
            | gzip -c > hg38.nasLar1.syn.chain.gz
hgLoadChain -tIndex hg38 chainSynNasLar1 hg38.nasLar1.syn.chain.gz
netFilter -minGap=10 hg38.nasLar1.syn.net.gz \
  | hgLoadNet -verbose=0 hg38 netSynNasLar1 stdin
cd /hive/data/genomes/hg38/bed/lastzNasLar1.2014-12-15
featureBits hg38 chainSynNasLar1Link > fb.hg38.chainSynNasLar1Link.txt 2>&1
cat fb.hg38.chainSynNasLar1Link.txt
# 1911545258 bases of 3049335806 (62.687%) in intersection

    # and for the swap:
    mkdir /hive/data/genomes/nasLar1/bed/blastz.hg38.swap
    cd /hive/data/genomes/nasLar1/bed/blastz.hg38.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/hg38/bed/lastzNasLar1.2014-12-15/DEF \
        -swap -chainMinScore=3000 -chainLinearGap=medium \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    #  real    616m45.774s

    cat fb.nasLar1.chainHg38Link.txt
    # 2157676376 bases of 2398172200 (89.972%) in intersection

    # did this in two parts when discovered this was running on ku,
    # stopped it there, then finished it off on hgwdev.
    time (doRecipBest.pl -buildDir=`pwd` nasLar1 hg38) > rbest.log 2>&1
    # real    119m16.828s
    # real    536m38.397s

#########################################################################
# LASTZ human/hg38 Tree shrew/tupBel1 - (DONE - 2014-12-15 - Hiram)
    mkdir /hive/data/genomes/hg38/bed/lastzTupBel1.2014-12-15
    cd /hive/data/genomes/hg38/bed/lastzTupBel1.2014-12-15

    cp -p \
/hive/users/hiram/multiz/100way/hg38.tupBel1/hg38.tupBel1.tuning.top400.txt \
     ./hg38.tupBel1.tuning.Q.txt

    cat << '_EOF_' > DEF
# human vs Tree shrew
# parameters obtained from a tuning run of lastz_D
# /hive/users/hiram/multiz/100way/hg38.tupBel1/hg38.tupBel1.tuning.top400.txt

BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.54/bin/lastz
BLASTZ_T=2
BLASTZ_O=400
BLASTZ_E=30
BLASTZ_M=254
BLASTZ_X=840
BLASTZ_Y=3400
BLASTZ_Q=/hive/data/genomes/hg38/bed/lastzTupBel1.2014-12-15/hg38.tupBel1.tuning.Q.txt
#       A     C     G     T
# A    84  -203   -96  -292
# C  -203   100  -204   -96
# G   -96  -204   100  -203
# T  -292   -96  -203    84

# TARGET: human hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CTGDIR=/hive/data/genomes/hg38/hg38.contigs.2bit
SEQ1_CTGLEN=/hive/data/genomes/hg38/hg38.contigs.chrom.sizes
SEQ1_LIFT=/hive/data/genomes/hg38/jkStuff/hg38.contigs.lift
SEQ1_CHUNK=40000000
SEQ1_LIMIT=10
SEQ1_LAP=10000

# QUERY: Tree shrew tupBel1
SEQ2_DIR=/hive/data/genomes/tupBel1/tupBel1.2bit
SEQ2_LEN=/hive/data/genomes/tupBel1/chrom.sizes
SEQ2_CHUNK=20000000
SEQ2_LIMIT=400
SEQ2_LAP=0

BASE=/hive/data/genomes/hg38/bed/lastzTupBel1.2014-12-15
TMPDIR=/dev/shm
'_EOF_'
    # << happy emacs

    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
        -chainMinScore=3000 -chainLinearGap=medium \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > do.log 2>&1
    # real    266m34.212s

    cat fb.hg38.chainTupBel1Link.txt
    # 753229970 bases of 3049335806 (24.701%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` hg38 tupBel1) > rbest.log 2>&1 &
    # real    29m25.353s

    # and for the swap:
    mkdir /hive/data/genomes/tupBel1/bed/blastz.hg38.swap
    cd /hive/data/genomes/tupBel1/bed/blastz.hg38.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/hg38/bed/lastzTupBel1.2014-12-15/DEF \
        -swap -chainMinScore=3000 -chainLinearGap=medium \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    #  real    192m16.970s

    cat fb.tupBel1.chainHg38Link.txt
    # 749930137 bases of 2137225476 (35.089%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` tupBel1 hg38) > rbest.log 2>&1
    # real    142m10.914s

#########################################################################
# LASTZ human/hg38 Mouse lemur/micMur1 - (DONE - 2014-12-19 - Hiram)
    # for some odd reason, these results were lost
    # the same procedure was re-run March 2015 in: lastzMicMur1.2015-03-17
    mkdir /hive/data/genomes/hg38/bed/lastzMicMur1.2014-12-19
    cd /hive/data/genomes/hg38/bed/lastzMicMur1.2014-12-19

    cp -p \
/hive/users/hiram/multiz/100way/hg38.micMur1/hg38.micMur1.tuning.top400.txt \
     ./hg38.micMur1.tuning.Q.txt

    cat << '_EOF_' > DEF
# human vs Mouse lemur
# parameters obtained from a tuning run of lastz_D
# /hive/users/hiram/multiz/100way/hg38.micMur1/hg38.micMur1.tuning.top400.txt

BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.54/bin/lastz
BLASTZ_T=2
BLASTZ_O=400
BLASTZ_E=30
BLASTZ_M=254
BLASTZ_X=1000
BLASTZ_Y=3400
BLASTZ_Q=/hive/data/genomes/hg38/bed/lastzMicMur1.2014-12-19/hg38.micMur1.tuning.Q.txt
#       A     C     G     T
# A   100  -159   -37  -128
# C  -159    93  -186   -37
# G   -37  -186    93  -159
# T  -128   -37  -159   100

# TARGET: human hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CTGDIR=/hive/data/genomes/hg38/hg38.contigs.2bit
SEQ1_CTGLEN=/hive/data/genomes/hg38/hg38.contigs.chrom.sizes
SEQ1_LIFT=/hive/data/genomes/hg38/jkStuff/hg38.contigs.lift
SEQ1_CHUNK=40000000
SEQ1_LIMIT=10
SEQ1_LAP=10000

# QUERY: Mouse lemur micMur1
SEQ2_DIR=/hive/data/genomes/micMur1/micMur1.2bit
SEQ2_LEN=/hive/data/genomes/micMur1/chrom.sizes
SEQ2_CHUNK=20000000
SEQ2_LIMIT=400
SEQ2_LAP=0

BASE=/hive/data/genomes/hg38/bed/lastzMicMur1.2014-12-19
TMPDIR=/dev/shm
'_EOF_'
    # << happy emacs

    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
        -chainMinScore=3000 -chainLinearGap=medium \
          -stop=net -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > net.log 2>&1
    # real    116m3.143s

    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
        -chainMinScore=3000 -chainLinearGap=medium \
       -continue=load -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > load.log 2>&1
    # real    50m58.488s

    cat fb.hg38.chainMicMur1Link.txt
    # 1300627579 bases of 3049335806 (42.653%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` hg38 micMur1) > rbest.log 2>&1 &
    # real    39m44.440s
    # the re-run:
    # real    35m41.014s

    # and for the swap:
    mkdir /hive/data/genomes/micMur1/bed/blastz.hg38.swap
    cd /hive/data/genomes/micMur1/bed/blastz.hg38.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/hg38/bed/lastzMicMur1.2014-12-19/DEF \
        -swap -chainMinScore=3000 -chainLinearGap=medium \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    #  real    223m37.152s

    cat fb.micMur1.chainHg38Link.txt
    # 1253236864 bases of 1852394361 (67.655%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` micMur1 hg38) > rbest.log 2>&1
    # real    182m5.563s

#########################################################################
# LASTZ human/hg38 vs. sheep/oviAri3 - (DONE - 2015-04-27 - Hiram)
    mkdir /hive/data/genomes/hg38/bed/lastzOviAri3.2015-04-27
    cd /hive/data/genomes/hg38/bed/lastzOviAri3.2015-04-27

    cat << '_EOF_' > DEF
# human vs sheep
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz
BLASTZ_T=2
BLASTZ_O=400
BLASTZ_E=30
BLASTZ_M=254
# default BLASTZ_Q score matrix:
#       A     C     G     T
# A    91  -114   -31  -123
# C  -114   100  -125   -31
# G   -31  -125   100  -114
# T  -123   -31  -114    91

# TARGET: human hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CTGDIR=/hive/data/genomes/hg38/hg38.contigs.2bit
SEQ1_CTGLEN=/hive/data/genomes/hg38/hg38.contigs.chrom.sizes
SEQ1_LIFT=/hive/data/genomes/hg38/jkStuff/hg38.contigs.lift
SEQ1_CHUNK=40000000
SEQ1_LIMIT=5
SEQ1_LAP=10000

# QUERY: Sheep oviAri3
SEQ2_DIR=/hive/data/genomes/oviAri3/oviAri3.2bit
SEQ2_LEN=/hive/data/genomes/oviAri3/chrom.sizes
SEQ2_CHUNK=20000000
SEQ2_LIMIT=40
SEQ2_LAP=0

BASE=/hive/data/genomes/hg38/bed/lastzOviAri3.2015-04-27
TMPDIR=/dev/shm
'_EOF_'
    # << happy emacs

    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
        -chainMinScore=3000 -chainLinearGap=medium \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > do.log 2>&1
    # real    527m8.200s

    cat fb.hg38.chainOviAri3Link.txt
    # 1382921590 bases of 3049335806 (45.352%) in intersection
    # replacing the previous tuned version:
    # 1256101876 bases of 3049335806 (41.193%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` hg38 oviAri3) > rbest.log 2>&1 &
    # real    68m34.171s

    # and for the swap:
    mkdir /hive/data/genomes/oviAri3/bed/blastz.hg38.swap
    cd /hive/data/genomes/oviAri3/bed/blastz.hg38.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/hg38/bed/lastzOviAri3.2015-04-27/DEF \
        -swap -chainMinScore=3000 -chainLinearGap=medium \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    #  real    98m39.757s

    cat fb.oviAri3.chainHg38Link.txt
    # 1312457473 bases of 2534335866 (51.787%) in intersection
    # replacing the previous tuned version:
    # 1193048482 bases of 2534335866 (47.075%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` oviAri3 hg38) > rbest.log 2>&1
    # real    47m50.965s

#########################################################################
# LASTZ human/hg38 vs. medaka/oryLat2 - (DONE - 2015-02-06 - Hiram)
    mkdir /hive/data/genomes/hg38/bed/lastzOryLat2.2015-02-06
    cd /hive/data/genomes/hg38/bed/lastzOryLat2.2015-02-06

    cat << '_EOF_' > DEF
# human vs medaka
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.54/bin/lastz
BLASTZ_Y=3400
BLASTZ_L=6000
BLASTZ_K=2200
BLASTZ_M=50
BLASTZ_Q=/scratch/data/blastz/HoxD55.q
#      A    C    G    T
#     91  -90  -25 -100
#    -90  100 -100  -25
#    -25 -100  100  -90
#   -100  -25  -90  91

# TARGET: human hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CTGDIR=/hive/data/genomes/hg38/hg38.contigs.2bit
SEQ1_CTGLEN=/hive/data/genomes/hg38/hg38.contigs.chrom.sizes
SEQ1_LIFT=/hive/data/genomes/hg38/jkStuff/hg38.contigs.lift
SEQ1_CHUNK=40000000
SEQ1_LIMIT=3
SEQ1_LAP=10000

# QUERY: medaka oryLat2
SEQ2_DIR=/hive/data/genomes/oryLat2/oryLat2.2bit
SEQ2_LEN=/hive/data/genomes/oryLat2/chrom.sizes
SEQ2_CHUNK=20000000
SEQ2_LIMIT=28
SEQ2_LAP=0

BASE=/hive/data/genomes/hg38/bed/lastzOryLat2.2015-02-06
TMPDIR=/dev/shm
'_EOF_'
    # << happy emacs

    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
        -chainMinScore=5000 -chainLinearGap=loose \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > do.log 2>&1
    # real    59m44.479s

    cat fb.hg38.chainOryLat2Link.txt
    # 61061549 bases of 3049335806 (2.002%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` hg38 oryLat2) > rbest.log 2>&1 &
    # real    5m38.658s

    # and for the swap:
    mkdir /hive/data/genomes/oryLat2/bed/blastz.hg38.swap
    cd /hive/data/genomes/oryLat2/bed/blastz.hg38.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/hg38/bed/lastzOryLat2.2015-02-06/DEF \
        -swap -chainMinScore=5000 -chainLinearGap=loose \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    #  real    9m23.499s

    cat fb.oryLat2.chainHg38Link.txt
    # 47994675 bases of 700386597 (6.853%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` oryLat2 hg38) > rbest.log 2>&1
    # real    5m47.982s

#########################################################################
# LASTZ human/hg38 vs. lizard/anoCar2 - (DONE - 2015-02-06 - Hiram)
    mkdir /hive/data/genomes/hg38/bed/lastzAnoCar2.2015-02-06
    cd /hive/data/genomes/hg38/bed/lastzAnoCar2.2015-02-06

    cat << '_EOF_' > DEF
# human vs lizard
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.54/bin/lastz
BLASTZ_Y=3400
BLASTZ_L=6000
BLASTZ_K=2200
BLASTZ_M=50
BLASTZ_Q=/scratch/data/blastz/HoxD55.q
#      A    C    G    T
#     91  -90  -25 -100
#    -90  100 -100  -25
#    -25 -100  100  -90
#   -100  -25  -90  91

# TARGET: human hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CTGDIR=/hive/data/genomes/hg38/hg38.contigs.2bit
SEQ1_CTGLEN=/hive/data/genomes/hg38/hg38.contigs.chrom.sizes
SEQ1_LIFT=/hive/data/genomes/hg38/jkStuff/hg38.contigs.lift
SEQ1_CHUNK=40000000
SEQ1_LIMIT=3
SEQ1_LAP=10000

# QUERY: lizard anoCar2
SEQ2_DIR=/hive/data/genomes/anoCar2/anoCar2.2bit
SEQ2_LEN=/hive/data/genomes/anoCar2/chrom.sizes
SEQ2_CHUNK=20000000
SEQ2_LIMIT=28
SEQ2_LAP=0

BASE=/hive/data/genomes/hg38/bed/lastzAnoCar2.2015-02-06
TMPDIR=/dev/shm
'_EOF_'
    # << happy emacs

    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
        -chainMinScore=5000 -chainLinearGap=loose \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > do.log 2>&1
    # real    279m15.159s

    cat fb.hg38.chainAnoCar2Link.txt
    # 109575794 bases of 3049335806 (3.593%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` hg38 anoCar2) > rbest.log 2>&1 &
    # real    17m23.686s

    # and for the swap:
    mkdir /hive/data/genomes/anoCar2/bed/blastz.hg38.swap
    cd /hive/data/genomes/anoCar2/bed/blastz.hg38.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/hg38/bed/lastzAnoCar2.2015-02-06/DEF \
        -swap -chainMinScore=5000 -chainLinearGap=loose \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    #  real    19m9.260s

    cat fb.anoCar2.chainHg38Link.txt
    # 88838401 bases of 1701353770 (5.222%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` anoCar2 hg38) > rbest.log 2>&1
    # real    7m31.302s

#########################################################################
# LASTZ human/hg38 vs. green seaturtle/cheMyd1 - (DONE - 2015-02-06 - Hiram)
    mkdir /hive/data/genomes/hg38/bed/lastzCheMyd1.2015-02-06
    cd /hive/data/genomes/hg38/bed/lastzCheMyd1.2015-02-06

    cat << '_EOF_' > DEF
# human vs green seaturtle
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.54/bin/lastz
BLASTZ_Y=3400
BLASTZ_L=6000
BLASTZ_K=2200
BLASTZ_M=50
BLASTZ_Q=/scratch/data/blastz/HoxD55.q
#      A    C    G    T
#     91  -90  -25 -100
#    -90  100 -100  -25
#    -25 -100  100  -90
#   -100  -25  -90  91

# TARGET: human hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CTGDIR=/hive/data/genomes/hg38/hg38.contigs.2bit
SEQ1_CTGLEN=/hive/data/genomes/hg38/hg38.contigs.chrom.sizes
SEQ1_LIFT=/hive/data/genomes/hg38/jkStuff/hg38.contigs.lift
SEQ1_CHUNK=40000000
SEQ1_LIMIT=3
SEQ1_LAP=10000

# QUERY: green seaturtle cheMyd1
SEQ2_DIR=/hive/data/genomes/cheMyd1/cheMyd1.2bit
SEQ2_LEN=/hive/data/genomes/cheMyd1/chrom.sizes
SEQ2_CHUNK=20000000
SEQ2_LIMIT=800
SEQ2_LAP=0

BASE=/hive/data/genomes/hg38/bed/lastzCheMyd1.2015-02-06
TMPDIR=/dev/shm
'_EOF_'
    # << happy emacs

    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
        -chainMinScore=5000 -chainLinearGap=loose \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > do.log 2>&1
    # real    274m42.880s

    cat fb.hg38.chainCheMyd1Link.txt
    # 191988160 bases of 3049335806 (6.296%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` hg38 cheMyd1) > rbest.log 2>&1 &
    # real    8m1.248s

    # and for the swap:
    mkdir /hive/data/genomes/cheMyd1/bed/blastz.hg38.swap
    cd /hive/data/genomes/cheMyd1/bed/blastz.hg38.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/hg38/bed/lastzCheMyd1.2015-02-06/DEF \
        -swap -chainMinScore=5000 -chainLinearGap=loose \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    #  real    35m32.831s

    cat fb.cheMyd1.chainHg38Link.txt
    # 167987740 bases of 2110381997 (7.960%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` cheMyd1 hg38) > rbest.log 2>&1
    # real    14m38.900s

#########################################################################
# LASTZ human/hg38 vs. painted turtle/chrPic2 - (DONE - 2015-02-06 - Hiram)
    mkdir /hive/data/genomes/hg38/bed/lastzChrPic2.2015-02-06
    cd /hive/data/genomes/hg38/bed/lastzChrPic2.2015-02-06

    cat << '_EOF_' > DEF
# human vs painted turtle
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.54/bin/lastz
BLASTZ_Y=3400
BLASTZ_L=6000
BLASTZ_K=2200
BLASTZ_M=50
BLASTZ_Q=/scratch/data/blastz/HoxD55.q
#      A    C    G    T
#     91  -90  -25 -100
#    -90  100 -100  -25
#    -25 -100  100  -90
#   -100  -25  -90  91

# TARGET: human hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CTGDIR=/hive/data/genomes/hg38/hg38.contigs.2bit
SEQ1_CTGLEN=/hive/data/genomes/hg38/hg38.contigs.chrom.sizes
SEQ1_LIFT=/hive/data/genomes/hg38/jkStuff/hg38.contigs.lift
SEQ1_CHUNK=40000000
SEQ1_LIMIT=3
SEQ1_LAP=10000

# QUERY: painted turtle chrPic2
SEQ2_DIR=/hive/data/genomes/chrPic2/chrPic2.2bit
SEQ2_LEN=/hive/data/genomes/chrPic2/chrom.sizes
SEQ2_CHUNK=20000000
SEQ2_LIMIT=400
SEQ2_LAP=0

BASE=/hive/data/genomes/hg38/bed/lastzChrPic2.2015-02-06
TMPDIR=/dev/shm
'_EOF_'
    # << happy emacs

    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
        -chainMinScore=5000 -chainLinearGap=loose \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > do.log 2>&1
    # real    286m29.793s

    cat fb.hg38.chainChrPic2Link.txt
    # 204556077 bases of 3049335806 (6.708%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` hg38 chrPic2) > rbest.log 2>&1 &
    # real    9m13.702s

    # and for the swap:
    mkdir /hive/data/genomes/chrPic2/bed/blastz.hg38.swap
    cd /hive/data/genomes/chrPic2/bed/blastz.hg38.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/hg38/bed/lastzChrPic2.2015-02-06/DEF \
        -swap -chainMinScore=5000 -chainLinearGap=loose \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    #  real    35m11.829s

    cat fb.chrPic2.chainHg38Link.txt
    # 185888111 bases of 2173204089 (8.554%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` chrPic2 hg38) > rbest.log 2>&1
    # real    15m17.351s

#########################################################################
# LASTZ human/hg38 vs. painted turtle/xipMac1 - (DONE - 2015-02-06 - Hiram)
    mkdir /hive/data/genomes/hg38/bed/lastzXipMac1.2015-02-06
    cd /hive/data/genomes/hg38/bed/lastzXipMac1.2015-02-06

    cat << '_EOF_' > DEF
# human vs painted turtle
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.54/bin/lastz
BLASTZ_Y=3400
BLASTZ_L=6000
BLASTZ_K=2200
BLASTZ_M=50
BLASTZ_Q=/scratch/data/blastz/HoxD55.q
#      A    C    G    T
#     91  -90  -25 -100
#    -90  100 -100  -25
#    -25 -100  100  -90
#   -100  -25  -90  91

# TARGET: human hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CTGDIR=/hive/data/genomes/hg38/hg38.contigs.2bit
SEQ1_CTGLEN=/hive/data/genomes/hg38/hg38.contigs.chrom.sizes
SEQ1_LIFT=/hive/data/genomes/hg38/jkStuff/hg38.contigs.lift
SEQ1_CHUNK=40000000
SEQ1_LIMIT=3
SEQ1_LAP=10000

# QUERY: painted turtle xipMac1
SEQ2_DIR=/hive/data/genomes/xipMac1/xipMac1.2bit
SEQ2_LEN=/hive/data/genomes/xipMac1/chrom.sizes
SEQ2_CHUNK=20000000
SEQ2_LIMIT=100
SEQ2_LAP=0

BASE=/hive/data/genomes/hg38/bed/lastzXipMac1.2015-02-06
TMPDIR=/dev/shm
'_EOF_'
    # << happy emacs

    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
        -chainMinScore=5000 -chainLinearGap=loose \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > do.log 2>&1
    # real    125m46.563s

    cat fb.hg38.chainXipMac1Link.txt
    # 57890952 bases of 3049335806 (1.898%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` hg38 xipMac1) > rbest.log 2>&1 &
    # real    3m48.235s

    # and for the swap:
    mkdir /hive/data/genomes/xipMac1/bed/blastz.hg38.swap
    cd /hive/data/genomes/xipMac1/bed/blastz.hg38.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/hg38/bed/lastzXipMac1.2015-02-06/DEF \
        -swap -chainMinScore=5000 -chainLinearGap=loose \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    #  real    9m11.951s

    cat fb.xipMac1.chainHg38Link.txt
    # 48535752 bases of 652815383 (7.435%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` xipMac1 hg38) > rbest.log 2>&1
    # real    6m4.065s

#########################################################################
# LASTZ human/hg38 vs. Pundamilia nyererei/punNye1 - (DONE - 2015-02-06 - Hiram)
    mkdir /hive/data/genomes/hg38/bed/lastzPunNye1.2015-02-06
    cd /hive/data/genomes/hg38/bed/lastzPunNye1.2015-02-06

    cat << '_EOF_' > DEF
# human vs Pundamilia nyererei
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.54/bin/lastz
BLASTZ_Y=3400
BLASTZ_L=6000
BLASTZ_K=2200
BLASTZ_M=50
BLASTZ_Q=/scratch/data/blastz/HoxD55.q
#      A    C    G    T
#     91  -90  -25 -100
#    -90  100 -100  -25
#    -25 -100  100  -90
#   -100  -25  -90  91

# TARGET: human hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CTGDIR=/hive/data/genomes/hg38/hg38.contigs.2bit
SEQ1_CTGLEN=/hive/data/genomes/hg38/hg38.contigs.chrom.sizes
SEQ1_LIFT=/hive/data/genomes/hg38/jkStuff/hg38.contigs.lift
SEQ1_CHUNK=40000000
SEQ1_LIMIT=3
SEQ1_LAP=10000

# QUERY: Pundamilia nyererei punNye1
SEQ2_DIR=/hive/data/genomes/punNye1/punNye1.2bit
SEQ2_LEN=/hive/data/genomes/punNye1/chrom.sizes
SEQ2_CHUNK=20000000
SEQ2_LIMIT=30
SEQ2_LAP=0

BASE=/hive/data/genomes/hg38/bed/lastzPunNye1.2015-02-06
TMPDIR=/dev/shm
'_EOF_'
    # << happy emacs

    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
        -chainMinScore=5000 -chainLinearGap=loose \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > do.log 2>&1
    # real    134m6.741s

    cat fb.hg38.chainPunNye1Link.txt
    # 54487438 bases of 3049335806 (1.787%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` hg38 punNye1) > rbest.log 2>&1 &
    # real    4m39.292s

    # and for the swap:
    mkdir /hive/data/genomes/punNye1/bed/blastz.hg38.swap
    cd /hive/data/genomes/punNye1/bed/blastz.hg38.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/hg38/bed/lastzPunNye1.2015-02-06/DEF \
        -swap -chainMinScore=5000 -chainLinearGap=loose \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    #  real    8m40.110s

    cat fb.punNye1.chainHg38Link.txt
    # 47965851 bases of 698757151 (6.864%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` punNye1 hg38) > rbest.log 2>&1
    # real    5m7.941s

#########################################################################
# LASTZ human/hg38 vs. Zebra Mbuna/mayZeb1 - (DONE - 2015-02-06 - Hiram)
    mkdir /hive/data/genomes/hg38/bed/lastzMayZeb1.2015-02-06
    cd /hive/data/genomes/hg38/bed/lastzMayZeb1.2015-02-06

    cat << '_EOF_' > DEF
# human vs Zebra Mbuna
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.54/bin/lastz
BLASTZ_Y=3400
BLASTZ_L=6000
BLASTZ_K=2200
BLASTZ_M=50
BLASTZ_Q=/scratch/data/blastz/HoxD55.q
#      A    C    G    T
#     91  -90  -25 -100
#    -90  100 -100  -25
#    -25 -100  100  -90
#   -100  -25  -90  91

# TARGET: human hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CTGDIR=/hive/data/genomes/hg38/hg38.contigs.2bit
SEQ1_CTGLEN=/hive/data/genomes/hg38/hg38.contigs.chrom.sizes
SEQ1_LIFT=/hive/data/genomes/hg38/jkStuff/hg38.contigs.lift
SEQ1_CHUNK=40000000
SEQ1_LIMIT=3
SEQ1_LAP=10000

# QUERY: Zebra Mbuna mayZeb1
SEQ2_DIR=/hive/data/genomes/mayZeb1/mayZeb1.2bit
SEQ2_LEN=/hive/data/genomes/mayZeb1/chrom.sizes
SEQ2_CHUNK=20000000
SEQ2_LIMIT=30
SEQ2_LAP=0

BASE=/hive/data/genomes/hg38/bed/lastzMayZeb1.2015-02-06
TMPDIR=/dev/shm
'_EOF_'
    # << happy emacs

    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
        -chainMinScore=5000 -chainLinearGap=loose \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > do.log 2>&1
    # real    1066m37.973s

    cat fb.hg38.chainMayZeb1Link.txt
    # 55052422 bases of 3049335806 (1.805%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` hg38 mayZeb1) > rbest.log 2>&1 &
    # real    4m49.016s

    # and for the swap:
    mkdir /hive/data/genomes/mayZeb1/bed/blastz.hg38.swap
    cd /hive/data/genomes/mayZeb1/bed/blastz.hg38.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/hg38/bed/lastzMayZeb1.2015-02-06/DEF \
        -swap -chainMinScore=5000 -chainLinearGap=loose \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    #  real    8m24.648s

    cat fb.mayZeb1.chainHg38Link.txt
    # 48376552 bases of 713527863 (6.780%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` mayZeb1 hg38) > rbest.log 2>&1
    # real    4m57.850s

#########################################################################
# LASTZ human/hg38 vs. zebrafish/danRer10 - (DONE - 2015-02-06 - Hiram)
    mkdir /hive/data/genomes/hg38/bed/lastzDanRer10.2015-02-06
    cd /hive/data/genomes/hg38/bed/lastzDanRer10.2015-02-06

    cat << '_EOF_' > DEF
# human vs zebrafish
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.54/bin/lastz
BLASTZ_Y=3400
BLASTZ_L=6000
BLASTZ_K=2200
BLASTZ_M=50
BLASTZ_Q=/scratch/data/blastz/HoxD55.q
#      A    C    G    T
#     91  -90  -25 -100
#    -90  100 -100  -25
#    -25 -100  100  -90
#   -100  -25  -90  91

# TARGET: human hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CTGDIR=/hive/data/genomes/hg38/hg38.contigs.2bit
SEQ1_CTGLEN=/hive/data/genomes/hg38/hg38.contigs.chrom.sizes
SEQ1_LIFT=/hive/data/genomes/hg38/jkStuff/hg38.contigs.lift
SEQ1_CHUNK=40000000
SEQ1_LIMIT=3
SEQ1_LAP=10000

# QUERY: zebrafish danRer10
SEQ2_DIR=/hive/data/genomes/danRer10/danRer10.2bit
SEQ2_LEN=/hive/data/genomes/danRer10/chrom.sizes
SEQ2_CHUNK=20000000
SEQ2_LIMIT=30
SEQ2_LAP=0

BASE=/hive/data/genomes/hg38/bed/lastzDanRer10.2015-02-06
TMPDIR=/dev/shm
'_EOF_'
    # << happy emacs

    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
        -chainMinScore=5000 -chainLinearGap=loose \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > do.log 2>&1
    # real    2785m54.894s

    cat fb.hg38.chainDanRer10Link.txt
    # 102378031 bases of 3049335806 (3.357%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` hg38 danRer10) > rbest.log 2>&1 &
    # real    7m50.594s

    # and for the swap:
    mkdir /hive/data/genomes/danRer10/bed/blastz.hg38.swap
    cd /hive/data/genomes/danRer10/bed/blastz.hg38.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/hg38/bed/lastzDanRer10.2015-02-06/DEF \
        -swap -chainMinScore=5000 -chainLinearGap=loose \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    #  real    37m50.204s

    cat fb.danRer10.chainHg38Link.txt
    # 97391181 bases of 1369683683 (7.110%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` danRer10 hg38) > rbest.log 2>&1
    # real    8m37.556s

#########################################################################
# LASTZ human/hg38 vs. lamprey/petMar2 - (DONE - 2015-02-06 - Hiram)
    mkdir /hive/data/genomes/hg38/bed/lastzPetMar2.2015-02-06
    cd /hive/data/genomes/hg38/bed/lastzPetMar2.2015-02-06

    cat << '_EOF_' > DEF
# human vs lamprey
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.54/bin/lastz
BLASTZ_Y=3400
BLASTZ_L=6000
BLASTZ_K=2200
BLASTZ_M=50
BLASTZ_Q=/scratch/data/blastz/HoxD55.q
#      A    C    G    T
#     91  -90  -25 -100
#    -90  100 -100  -25
#    -25 -100  100  -90
#   -100  -25  -90  91

# TARGET: human hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CTGDIR=/hive/data/genomes/hg38/hg38.contigs.2bit
SEQ1_CTGLEN=/hive/data/genomes/hg38/hg38.contigs.chrom.sizes
SEQ1_LIFT=/hive/data/genomes/hg38/jkStuff/hg38.contigs.lift
SEQ1_CHUNK=40000000
SEQ1_LIMIT=3
SEQ1_LAP=10000

# QUERY: lamprey petMar2
SEQ2_DIR=/hive/data/genomes/petMar2/petMar2.2bit
SEQ2_LEN=/hive/data/genomes/petMar2/chrom.sizes
SEQ2_CHUNK=20000000
SEQ2_LIMIT=100
SEQ2_LAP=0

BASE=/hive/data/genomes/hg38/bed/lastzPetMar2.2015-02-06
TMPDIR=/dev/shm
'_EOF_'
    # << happy emacs

    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
        -chainMinScore=5000 -chainLinearGap=loose \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > do.log 2>&1
    # real    120m15.847s

    cat fb.hg38.chainPetMar2Link.txt
    # 38581766 bases of 3049335806 (1.265%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` hg38 petMar2) > rbest.log 2>&1 &
    # real    2m51.935s

    # and for the swap:
    mkdir /hive/data/genomes/petMar2/bed/blastz.hg38.swap
    cd /hive/data/genomes/petMar2/bed/blastz.hg38.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/hg38/bed/lastzPetMar2.2015-02-06/DEF \
        -swap -chainMinScore=5000 -chainLinearGap=loose \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    #  real    8m48.057s

    cat fb.petMar2.chainHg38Link.txt
    # 25633579 bases of 647368134 (3.960%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` petMar2 hg38) > rbest.log 2>&1
    # real    4m46.757s

#########################################################################
# LASTZ human/hg38 vs. Aardvark/oryAfe1 - (DONE - 2015-04-23 - Hiram)
    mkdir /hive/data/genomes/hg38/bed/lastzOryAfe1.2015-04-23
    cd /hive/data/genomes/hg38/bed/lastzOryAfe1.2015-04-23

    cat << '_EOF_' > DEF
# human vs Aardvark
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz
BLASTZ_O=400
BLASTZ_E=30
BLASTZ_M=254
# default BLASTZ_Q score matrix:
#       A     C     G     T
# A    91  -114   -31  -123
# C  -114   100  -125   -31
# G   -31  -125   100  -114
# T  -123   -31  -114    91

# TARGET: human hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CTGDIR=/hive/data/genomes/hg38/hg38.contigs.2bit
SEQ1_CTGLEN=/hive/data/genomes/hg38/hg38.contigs.chrom.sizes
SEQ1_LIFT=/hive/data/genomes/hg38/jkStuff/hg38.contigs.lift
SEQ1_CHUNK=40000000
SEQ1_LIMIT=10
SEQ1_LAP=10000

# QUERY: Aardvark oryAfe1
SEQ2_DIR=/hive/data/genomes/oryAfe1/oryAfe1.2bit
SEQ2_LEN=/hive/data/genomes/oryAfe1/chrom.sizes
SEQ2_CHUNK=20000000
SEQ2_LIMIT=100
SEQ2_LAP=0

BASE=/hive/data/genomes/hg38/bed/lastzOryAfe1.2015-04-23
TMPDIR=/dev/shm
'_EOF_'
    # << happy emacs

    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
        -chainMinScore=3000 -chainLinearGap=medium \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > do.log 2>&1
    #  real    472m21.083s

    cat fb.hg38.chainOryAfe1Link.txt
    # 1236908970 bases of 3049335806 (40.563%) in intersection
    # replacing previous tuned version:
    # 1113801383 bases of 3049335806 (36.526%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` hg38 oryAfe1) > rbest.log 2>&1 &
    # real    34m51.856s

    # and for the swap:
    mkdir /hive/data/genomes/oryAfe1/bed/blastz.hg38.swap
    cd /hive/data/genomes/oryAfe1/bed/blastz.hg38.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/hg38/bed/lastzOryAfe1.2015-04-23/DEF \
        -swap -chainMinScore=3000 -chainLinearGap=medium \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    #  real    105m58.107s

    cat fb.oryAfe1.chainHg38Link.txt
    # 1164699059 bases of 3415340621 (34.102%) in intersection
    # replacing previous tuned version:
    # 1048528734 bases of 3415340621 (30.701%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` oryAfe1 hg38) > rbest.log 2>&1
    # real    38m36.380s

#########################################################################
# LASTZ human/hg38 vs. White rhinoceros/cerSim1 - (DONE - 2015-02-22 - Hiram)
    mkdir /hive/data/genomes/hg38/bed/lastzCerSim1.2015-02-22
    cd /hive/data/genomes/hg38/bed/lastzCerSim1.2015-02-22

    cat << '_EOF_' > DEF
# human vs White rhinoceros
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz
BLASTZ_O=400
BLASTZ_E=30
BLASTZ_M=254
# default BLASTZ_Q score matrix:
#       A     C     G     T
# A    91  -114   -31  -123
# C  -114   100  -125   -31
# G   -31  -125   100  -114
# T  -123   -31  -114    91

# TARGET: human hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CTGDIR=/hive/data/genomes/hg38/hg38.contigs.2bit
SEQ1_CTGLEN=/hive/data/genomes/hg38/hg38.contigs.chrom.sizes
SEQ1_LIFT=/hive/data/genomes/hg38/jkStuff/hg38.contigs.lift
SEQ1_CHUNK=40000000
SEQ1_LIMIT=5
SEQ1_LAP=10000

# QUERY: White rhinoceros cerSim1
SEQ2_DIR=/hive/data/genomes/cerSim1/cerSim1.2bit
SEQ2_LEN=/hive/data/genomes/cerSim1/chrom.sizes
SEQ2_CHUNK=20000000
SEQ2_LIMIT=20
SEQ2_LAP=0

BASE=/hive/data/genomes/hg38/bed/lastzCerSim1.2015-02-22
TMPDIR=/dev/shm
'_EOF_'
    # << happy emacs

    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
        -chainMinScore=3000 -chainLinearGap=medium \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > do.log 2>&1
    # real    1227m14.067s

    cat fb.hg38.chainCerSim1Link.txt
    # 1726920355 bases of 3049335806 (56.633%) in intersection
    # replacing previous tuned version:
    # 1618425081 bases of 3049335806 (53.075%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` hg38 cerSim1) > rbest.log 2>&1 &
    # real    42m41.811s

    # and for the swap:
    mkdir /hive/data/genomes/cerSim1/bed/blastz.hg38.swap
    cd /hive/data/genomes/cerSim1/bed/blastz.hg38.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/hg38/bed/lastzCerSim1.2015-02-22/DEF \
        -swap -chainMinScore=3000 -chainLinearGap=medium \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    # real    117m59.898s

    cat fb.cerSim1.chainHg38Link.txt
    # 1638614141 bases of 2366858012 (69.232%) in intersection
    # replacing previous tuned version:
    # 1534238724 bases of 2366858012 (64.822%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` cerSim1 hg38) > rbest.log 2>&1
    # real    78m9.790s

#########################################################################
# LASTZ human/hg38 vs. Cape golden mole/chrAsi1 - (DONE - 2015-02-17 - Hiram)
    mkdir /hive/data/genomes/hg38/bed/lastzChrAsi1.2015-02-17
    cd /hive/data/genomes/hg38/bed/lastzChrAsi1.2015-02-17

    cat << '_EOF_' > DEF
# human vs Cape golden mole
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.54/bin/lastz
BLASTZ_O=400
BLASTZ_E=30

# TARGET: human hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CTGDIR=/hive/data/genomes/hg38/hg38.contigs.2bit
SEQ1_CTGLEN=/hive/data/genomes/hg38/hg38.contigs.chrom.sizes
SEQ1_LIFT=/hive/data/genomes/hg38/jkStuff/hg38.contigs.lift
SEQ1_CHUNK=40000000
SEQ1_LIMIT=10
SEQ1_LAP=10000

# QUERY: Cape golden mole chrAsi1
SEQ2_DIR=/hive/data/genomes/chrAsi1/chrAsi1.2bit
SEQ2_LEN=/hive/data/genomes/chrAsi1/chrom.sizes
SEQ2_CHUNK=20000000
SEQ2_LIMIT=100
SEQ2_LAP=0

BASE=/hive/data/genomes/hg38/bed/lastzChrAsi1.2015-02-17
TMPDIR=/dev/shm
'_EOF_'
    # << happy emacs

    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
        -chainMinScore=3000 -chainLinearGap=medium \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > do.log 2>&1
    # real    3754m43.142s

    cat fb.hg38.chainChrAsi1Link.txt
    # 1015855213 bases of 3049335806 (33.314%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` hg38 chrAsi1) \
       > rbest.log 2>&1 &
    # real    42m12.650s

    # and for the swap:
    mkdir /hive/data/genomes/chrAsi1/bed/blastz.hg38.swap
    cd /hive/data/genomes/chrAsi1/bed/blastz.hg38.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/hg38/bed/lastzChrAsi1.2015-02-17/DEF \
        -swap -chainMinScore=3000 -chainLinearGap=medium \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    #  real    103m1.384s

    cat fb.chrAsi1.chainHg38Link.txt
    # 977711721 bases of 3363564316 (29.068%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` chrAsi1 hg38) \
       > rbest.log 2>&1
    # real    47m40.074s

#########################################################################
# LASTZ human/hg38 vs. Big brown bat/eptFus1 - (DONE - 2015-04-24 - Hiram)
    mkdir /hive/data/genomes/hg38/bed/lastzEptFus1.2015-04-24
    cd /hive/data/genomes/hg38/bed/lastzEptFus1.2015-04-24

    cat << '_EOF_' > DEF
# human vs Big brown bat
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz
BLASTZ_O=400
BLASTZ_E=30
BLASTZ_M=254
# default BLASTZ_Q score matrix:
#       A     C     G     T
# A    91  -114   -31  -123
# C  -114   100  -125   -31
# G   -31  -125   100  -114
# T  -123   -31  -114    91

# TARGET: human hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CTGDIR=/hive/data/genomes/hg38/hg38.contigs.2bit
SEQ1_CTGLEN=/hive/data/genomes/hg38/hg38.contigs.chrom.sizes
SEQ1_LIFT=/hive/data/genomes/hg38/jkStuff/hg38.contigs.lift
SEQ1_CHUNK=40000000
SEQ1_LIMIT=10
SEQ1_LAP=10000

# QUERY: Big brown bat eptFus1
SEQ2_DIR=/hive/data/genomes/eptFus1/eptFus1.2bit
SEQ2_LEN=/hive/data/genomes/eptFus1/chrom.sizes
SEQ2_CHUNK=20000000
SEQ2_LIMIT=20
SEQ2_LAP=0

BASE=/hive/data/genomes/hg38/bed/lastzEptFus1.2015-04-24
TMPDIR=/dev/shm
'_EOF_'
    # << happy emacs

    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
        -chainMinScore=3000 -chainLinearGap=medium \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > do.log 2>&1
    # real    377m2.703s

    cat fb.hg38.chainEptFus1Link.txt
    # 1193001967 bases of 3049335806 (39.123%) in intersection
    # replacing previous tuned version:
    # 1109543782 bases of 3049335806 (36.386%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` hg38 eptFus1) > rbest.log 2>&1 &
    # real    33m10.892s

    # and for the swap:
    mkdir /hive/data/genomes/eptFus1/bed/blastz.hg38.swap
    cd /hive/data/genomes/eptFus1/bed/blastz.hg38.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/hg38/bed/lastzEptFus1.2015-04-24/DEF \
        -swap -chainMinScore=3000 -chainLinearGap=medium \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    #  real    91m1.466s

    cat fb.eptFus1.chainHg38Link.txt
    # 1127211856 bases of 1811378799 (62.229%) in intersection
    # replacing previous tuned version:
    # 1051896885 bases of 1811378799 (58.072%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` eptFus1 hg38) > rbest.log 2>&1
    # real    36m31.110s

#########################################################################
# LASTZ human/hg38 vs. Chinese tree shrew/tupChi1 - (DONE - 2015-02-17 - Hiram)
    mkdir /hive/data/genomes/hg38/bed/lastzTupChi1.2015-02-17
    cd /hive/data/genomes/hg38/bed/lastzTupChi1.2015-02-17

    cat << '_EOF_' > DEF
# human vs Chinese tree shrew
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.54/bin/lastz
BLASTZ_O=400
BLASTZ_E=30

# TARGET: human hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CTGDIR=/hive/data/genomes/hg38/hg38.contigs.2bit
SEQ1_CTGLEN=/hive/data/genomes/hg38/hg38.contigs.chrom.sizes
SEQ1_LIFT=/hive/data/genomes/hg38/jkStuff/hg38.contigs.lift
SEQ1_CHUNK=40000000
SEQ1_LIMIT=20
SEQ1_LAP=10000

# QUERY: Chinese tree shrew tupChi1
SEQ2_DIR=/hive/data/genomes/tupChi1/tupChi1.2bit
SEQ2_LEN=/hive/data/genomes/tupChi1/chrom.sizes
SEQ2_CHUNK=20000000
SEQ2_LIMIT=120
SEQ2_LAP=0

BASE=/hive/data/genomes/hg38/bed/lastzTupChi1.2015-02-17
TMPDIR=/dev/shm
'_EOF_'
    # << happy emacs

    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
        -chainMinScore=3000 -chainLinearGap=medium \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > do.log 2>&1
    # real    2638m13.806s

    cat fb.hg38.chainTupChi1Link.txt
    # 1379994626 bases of 3049335806 (45.256%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` hg38 tupChi1) \
       > rbest.log 2>&1 &
    # real    60m22.301s

    # and for the swap:
    mkdir /hive/data/genomes/tupChi1/bed/blastz.hg38.swap
    cd /hive/data/genomes/tupChi1/bed/blastz.hg38.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/hg38/bed/lastzTupChi1.2015-02-17/DEF \
        -swap -chainMinScore=3000 -chainLinearGap=medium \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    #  real    119m54.935s

    cat fb.tupChi1.chainHg38Link.txt
    # 1362665822 bases of 2706389135 (50.350%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` tupChi1 hg38) > rbest.log 2>&1
    # real    43m38.032s

#########################################################################
# LASTZ human/hg38 vs. horse/equCab2 - (DONE - 2015-02-22 - Hiram)
    mkdir /hive/data/genomes/hg38/bed/lastzEquCab2.2015-02-22
    cd /hive/data/genomes/hg38/bed/lastzEquCab2.2015-02-22

    cat << '_EOF_' > DEF
# human vs horse
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz
BLASTZ_O=400
BLASTZ_E=30
BLASTZ_M=254
# default BLASTZ_Q score matrix:
#       A     C     G     T
# A    91  -114   -31  -123
# C  -114   100  -125   -31
# G   -31  -125   100  -114
# T  -123   -31  -114    91

# TARGET: human hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CTGDIR=/hive/data/genomes/hg38/hg38.contigs.2bit
SEQ1_CTGLEN=/hive/data/genomes/hg38/hg38.contigs.chrom.sizes
SEQ1_LIFT=/hive/data/genomes/hg38/jkStuff/hg38.contigs.lift
SEQ1_CHUNK=40000000
SEQ1_LIMIT=20
SEQ1_LAP=10000

# QUERY: horse equCab2
SEQ2_DIR=/hive/data/genomes/equCab2/equCab2.2bit
SEQ2_LEN=/hive/data/genomes/equCab2/chrom.sizes
SEQ2_CHUNK=20000000
SEQ2_LIMIT=10
SEQ2_LAP=0

BASE=/hive/data/genomes/hg38/bed/lastzEquCab2.2015-02-22
TMPDIR=/dev/shm
'_EOF_'
    # << happy emacs

    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
        -chainMinScore=3000 -chainLinearGap=medium \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > do.log 2>&1
    # real    966m54.143s

    cat fb.hg38.chainEquCab2Link.txt
    # 1691134629 bases of 3049335806 (55.459%) in intersection
    # replacing the previous tuned version:
    # 1588178706 bases of 3049335806 (52.083%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` hg38 equCab2) > rbest.log 2>&1 &
    # real    81m49.399s

    # load up the recip best chainNet tables
    time (doRecipBest.pl -load -continue=load -workhorse=hgwdev \
	-buildDir=`pwd` hg38 equCab2) > loadRBest.log 2>&1 &
    # real    11m38.247s
    cat fb.hg38.chainRBestEquCab2Link.txt
# 1547949213 bases of 3049335806 (50.763%) in intersection

    # create and load up the syntenic chainNet tables 2017-10-30
cd /hive/data/genomes/hg38/bed/lastzEquCab2.2015-02-22/axtChain
netToAxt hg38.equCab2.syn.net.gz hg38.equCab2.all.chain.gz \
/scratch/data/hg38/hg38.2bit /hive/data/genomes/equCab2/equCab2.2bit stdout \
  | axtSort stdin stdout \
     | axtToChain stdin /hive/data/genomes/hg38/chrom.sizes \
        /hive/data/genomes/equCab2/chrom.sizes stdout \
            | gzip -c > hg38.equCab2.syn.chain.gz
hgLoadChain -tIndex hg38 chainSynEquCab2 hg38.equCab2.syn.chain.gz
netFilter -minGap=10 hg38.equCab2.syn.net.gz \
  | hgLoadNet -verbose=0 hg38 netSynEquCab2 stdin
cd /hive/data/genomes/hg38/bed/lastzEquCab2.2015-02-22
featureBits hg38 chainSynEquCab2Link > fb.hg38.chainSynEquCab2Link.txt 2>&1
cat fb.hg38.chainSynEquCab2Link.txt
# 1625260798 bases of 3049335806 (53.299%) in intersection

    # and for the swap:
    mkdir /hive/data/genomes/equCab2/bed/blastz.hg38.swap
    cd /hive/data/genomes/equCab2/bed/blastz.hg38.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/hg38/bed/lastzEquCab2.2015-02-22/DEF \
        -swap -chainMinScore=3000 -chainLinearGap=medium \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    #  real    123m57.167s

    cat fb.equCab2.chainHg38Link.txt
    # 1617562865 bases of 2428790173 (66.600%) in intersection
    # replacing the previous tuned version:
    # 1516707888 bases of 2428790173 (62.447%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` equCab2 hg38) > rbest.log 2>&1
    # real    43m47.647s

#########################################################################
# LASTZ human/hg38 vs. Bactrian camel/camFer1 - (DONE - 2015-04-24 - Hiram)
    mkdir /hive/data/genomes/hg38/bed/lastzCamFer1.2015-04-24
    cd /hive/data/genomes/hg38/bed/lastzCamFer1.2015-04-24

    cat << '_EOF_' > DEF
# human vs Bactrian camel
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz
BLASTZ_O=400
BLASTZ_E=30
BLASTZ_M=254
# default BLASTZ_Q score matrix:
#       A     C     G     T
# A    91  -114   -31  -123
# C  -114   100  -125   -31
# G   -31  -125   100  -114
# T  -123   -31  -114    91

# TARGET: human hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CTGDIR=/hive/data/genomes/hg38/hg38.contigs.2bit
SEQ1_CTGLEN=/hive/data/genomes/hg38/hg38.contigs.chrom.sizes
SEQ1_LIFT=/hive/data/genomes/hg38/jkStuff/hg38.contigs.lift
SEQ1_CHUNK=40000000
SEQ1_LIMIT=20
SEQ1_LAP=10000

# QUERY: Bactrian camel camFer1
SEQ2_DIR=/hive/data/genomes/camFer1/camFer1.2bit
SEQ2_LEN=/hive/data/genomes/camFer1/chrom.sizes
SEQ2_CHUNK=20000000
SEQ2_LIMIT=20
SEQ2_LAP=0

BASE=/hive/data/genomes/hg38/bed/lastzCamFer1.2015-04-24
TMPDIR=/dev/shm
'_EOF_'
    # << happy emacs

    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
        -chainMinScore=3000 -chainLinearGap=medium \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > do.log 2>&1
    # real    382m39.001s


    cat fb.hg38.chainCamFer1Link.txt
    # 1497063551 bases of 3049335806 (49.095%) in intersection
    # replacing the previous tuned version:
    # 1408973544 bases of 3049335806 (46.206%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` hg38 camFer1) > rbest.log 2>&1 &
    # real    41m32.785s

    # and for the swap:
    mkdir /hive/data/genomes/camFer1/bed/blastz.hg38.swap
    cd /hive/data/genomes/camFer1/bed/blastz.hg38.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/hg38/bed/lastzCamFer1.2015-04-24/DEF \
        -swap -chainMinScore=3000 -chainLinearGap=medium \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    #  real    99m10.651s

    cat fb.camFer1.chainHg38Link.txt
    # 1414980564 bases of 1985442806 (71.268%) in intersection
    # replacing the previous tuned version:
    # 1335694086 bases of 1985442806 (67.274%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` camFer1 hg38) > rbest.log 2>&1
    # real    40m5.483s

#########################################################################
# LASTZ human/hg38 vs. alpaca/vicPac2 - (DONE - 2015-04-28 - Hiram)
    mkdir /hive/data/genomes/hg38/bed/lastzVicPac2.2015-04-28
    cd /hive/data/genomes/hg38/bed/lastzVicPac2.2015-04-28

    cat << '_EOF_' > DEF
# human vs alpaca
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz
BLASTZ_O=400
BLASTZ_E=30
BLASTZ_M=254
# default BLASTZ_Q score matrix:
#       A     C     G     T
# A    91  -114   -31  -123
# C  -114   100  -125   -31
# G   -31  -125   100  -114
# T  -123   -31  -114    91

# TARGET: human hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CTGDIR=/hive/data/genomes/hg38/hg38.contigs.2bit
SEQ1_CTGLEN=/hive/data/genomes/hg38/hg38.contigs.chrom.sizes
SEQ1_LIFT=/hive/data/genomes/hg38/jkStuff/hg38.contigs.lift
SEQ1_CHUNK=40000000
SEQ1_LIMIT=30
SEQ1_LAP=10000

# QUERY: alpaca vicPac2
SEQ2_DIR=/hive/data/genomes/vicPac2/vicPac2.2bit
SEQ2_LEN=/hive/data/genomes/vicPac2/chrom.sizes
SEQ2_CHUNK=20000000
SEQ2_LIMIT=400
SEQ2_LAP=0

BASE=/hive/data/genomes/hg38/bed/lastzVicPac2.2015-04-28
TMPDIR=/dev/shm
'_EOF_'
    # << happy emacs

    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
        -chainMinScore=3000 -chainLinearGap=medium \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > do.log 2>&1
    # real    1562m13.104s

    cat fb.hg38.chainVicPac2Link.txt
    # 1491400921 bases of 3049335806 (48.909%) in intersection
    # replacing the previous tuned version:
    # 1399262189 bases of 3049335806 (45.887%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` hg38 vicPac2) > rbest.log 2>&1 &
    # real    39m21.890s

    # and for the swap:
    mkdir /hive/data/genomes/vicPac2/bed/blastz.hg38.swap
    cd /hive/data/genomes/vicPac2/bed/blastz.hg38.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/hg38/bed/lastzVicPac2.2015-04-28/DEF \
        -swap -chainMinScore=3000 -chainLinearGap=medium \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    #  real    229m47.891s

    cat fb.vicPac2.chainHg38Link.txt
    # 1429121865 bases of 2078582856 (68.755%) in intersection
    # replacing the previous tuned version:
    # 1342041434 bases of 2078582856 (64.565%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` vicPac2 hg38) > rbest.log 2>&1
    # real    364m14.802s finished manually real    101m13.133s
    time (doRecipBest.pl -workhorse=hgwdev -continue=download \
       -buildDir=`pwd` vicPac2 hg38) > rbestDownload.log 2>&1
    # real    0m4.424s

#########################################################################
# LASTZ human/hg38 vs. dolphin/turTru2 - (DONE - 2015-04-28 - Hiram)
    mkdir /hive/data/genomes/hg38/bed/lastzTurTru2.2015-04-28
    cd /hive/data/genomes/hg38/bed/lastzTurTru2.2015-04-28

    cat << '_EOF_' > DEF
# human vs dolphin
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz
BLASTZ_O=400
BLASTZ_E=30
BLASTZ_M=254
# default BLASTZ_Q score matrix:
#       A     C     G     T
# A    91  -114   -31  -123
# C  -114   100  -125   -31
# G   -31  -125   100  -114
# T  -123   -31  -114    91

# TARGET: human hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CTGDIR=/hive/data/genomes/hg38/hg38.contigs.2bit
SEQ1_CTGLEN=/hive/data/genomes/hg38/hg38.contigs.chrom.sizes
SEQ1_LIFT=/hive/data/genomes/hg38/jkStuff/hg38.contigs.lift
SEQ1_CHUNK=40000000
SEQ1_LIMIT=30
SEQ1_LAP=10000

# QUERY: dolphin turTru2
SEQ2_DIR=/hive/data/genomes/turTru2/turTru2.2bit
SEQ2_LEN=/hive/data/genomes/turTru2/chrom.sizes
SEQ2_CHUNK=20000000
SEQ2_LIMIT=400
SEQ2_LAP=0

BASE=/hive/data/genomes/hg38/bed/lastzTurTru2.2015-04-28
TMPDIR=/dev/shm
'_EOF_'
    # << happy emacs

    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
        -chainMinScore=3000 -chainLinearGap=medium \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > do.log 2>&1
    # real    1495m0.218s

    cat fb.hg38.chainTurTru2Link.txt
    # 1516370469 bases of 3049335806 (49.728%) in intersection
    # replacing the previous tuned version:
    # 1404889155 bases of 3049335806 (46.072%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` hg38 turTru2) > rbest.log 2>&1 &
    # real    40m22.097s

    # and for the swap:
    mkdir /hive/data/genomes/turTru2/bed/blastz.hg38.swap
    cd /hive/data/genomes/turTru2/bed/blastz.hg38.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/hg38/bed/lastzTurTru2.2015-04-28/DEF \
        -swap -chainMinScore=3000 -chainLinearGap=medium \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    #  real    253m58.332s

    cat fb.turTru2.chainHg38Link.txt
    # 1431921957 bases of 2332402443 (61.393%) in intersection
    # replacing the previous tuned version:
    # 1329424627 bases of 2332402443 (56.998%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` turTru2 hg38) > rbest.log 2>&1
    # real    119m47.159s

#########################################################################
# LASTZ human/hg38 vs. Killer whale/orcOrc1 - (DONE - 2015-04-28 - Hiram)
    mkdir /hive/data/genomes/hg38/bed/lastzOrcOrc1.2015-04-28
    cd /hive/data/genomes/hg38/bed/lastzOrcOrc1.2015-04-28

    cat << '_EOF_' > DEF
# human vs Killer whale
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz
BLASTZ_O=400
BLASTZ_E=30
BLASTZ_M=254
# default BLASTZ_Q score matrix:
#       A     C     G     T
# A    91  -114   -31  -123
# C  -114   100  -125   -31
# G   -31  -125   100  -114
# T  -123   -31  -114    91

# TARGET: human hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CTGDIR=/hive/data/genomes/hg38/hg38.contigs.2bit
SEQ1_CTGLEN=/hive/data/genomes/hg38/hg38.contigs.chrom.sizes
SEQ1_LIFT=/hive/data/genomes/hg38/jkStuff/hg38.contigs.lift
SEQ1_CHUNK=40000000
SEQ1_LIMIT=30
SEQ1_LAP=10000

# QUERY: Killer whale orcOrc1
SEQ2_DIR=/hive/data/genomes/orcOrc1/orcOrc1.2bit
SEQ2_LEN=/hive/data/genomes/orcOrc1/chrom.sizes
SEQ2_CHUNK=20000000
SEQ2_LIMIT=5
SEQ2_LAP=0

BASE=/hive/data/genomes/hg38/bed/lastzOrcOrc1.2015-04-28
TMPDIR=/dev/shm
'_EOF_'
    # << happy emacs

    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
        -chainMinScore=3000 -chainLinearGap=medium \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > do.log 2>&1
    # real    1874m13.873s

    cat fb.hg38.chainOrcOrc1Link.txt
    # 1546274677 bases of 3049335806 (50.709%) in intersection
    # replacing the previous tuned version:
    # 1441746760 bases of 3049335806 (47.281%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` hg38 orcOrc1) > rbest.log 2>&1 &
    # real    43m21.901s

    # and for the swap:
    mkdir /hive/data/genomes/orcOrc1/bed/blastz.hg38.swap
    cd /hive/data/genomes/orcOrc1/bed/blastz.hg38.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/hg38/bed/lastzOrcOrc1.2015-04-28/DEF \
        -swap -chainMinScore=3000 -chainLinearGap=medium \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    #  real    100m56.186s

    cat fb.orcOrc1.chainHg38Link.txt
    # 1447927506 bases of 2249582127 (64.364%) in intersection
    # replacing the previous tuned version:
    # 1354015119 bases of 2249582127 (60.190%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` orcOrc1 hg38) > rbest.log 2>&1
    # real    41m38.435s

#########################################################################
# LASTZ human/hg38 vs. squirrel/speTri2 - (DONE - 2015-04-28 - Hiram)
    mkdir /hive/data/genomes/hg38/bed/lastzSpeTri2.2015-04-28
    cd /hive/data/genomes/hg38/bed/lastzSpeTri2.2015-04-28

    cat << '_EOF_' > DEF
# human vs squirrel
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz
BLASTZ_O=400
BLASTZ_E=30
BLASTZ_M=254
# default BLASTZ_Q score matrix:
#       A     C     G     T
# A    91  -114   -31  -123
# C  -114   100  -125   -31
# G   -31  -125   100  -114
# T  -123   -31  -114    91

# TARGET: human hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CTGDIR=/hive/data/genomes/hg38/hg38.contigs.2bit
SEQ1_CTGLEN=/hive/data/genomes/hg38/hg38.contigs.chrom.sizes
SEQ1_LIFT=/hive/data/genomes/hg38/jkStuff/hg38.contigs.lift
SEQ1_CHUNK=40000000
SEQ1_LIMIT=30
SEQ1_LAP=10000

# QUERY: squirrel speTri2
SEQ2_DIR=/hive/data/genomes/speTri2/speTri2.2bit
SEQ2_LEN=/hive/data/genomes/speTri2/chrom.sizes
SEQ2_CHUNK=20000000
SEQ2_LIMIT=20
SEQ2_LAP=0

BASE=/hive/data/genomes/hg38/bed/lastzSpeTri2.2015-04-28
TMPDIR=/dev/shm
'_EOF_'
    # << happy emacs

    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
        -chainMinScore=3000 -chainLinearGap=medium \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > do.log 2>&1
    # real    1669m55.874s

    cat fb.hg38.chainSpeTri2Link.txt
    # 1472314467 bases of 3049335806 (48.283%) in intersection
    # replacing the previous tuned version:
    # 1363949428 bases of 3049335806 (44.729%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` hg38 speTri2) > rbest.log 2>&1 &
    # real    47m19.925s

    # and for the swap:
    mkdir /hive/data/genomes/speTri2/bed/blastz.hg38.swap
    cd /hive/data/genomes/speTri2/bed/blastz.hg38.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/hg38/bed/lastzSpeTri2.2015-04-28/DEF \
        -swap -chainMinScore=3000 -chainLinearGap=medium \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    #  real    114m57.250s

    cat fb.speTri2.chainHg38Link.txt
    # 1429491323 bases of 2311060300 (61.854%) in intersection
    # replacing the previous tuned version:
    # 1323562747 bases of 2311060300 (57.271%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` speTri2 hg38) > rbest.log 2>&1
    # real    46m47.951s

#########################################################################
# LASTZ human/hg38 vs. Black flying fox/pteAle1 - (DONE - 2015-04-28 - Hiram)
    mkdir /hive/data/genomes/hg38/bed/lastzPteAle1.2015-04-28
    cd /hive/data/genomes/hg38/bed/lastzPteAle1.2015-04-28

    cat << '_EOF_' > DEF
# human vs Black flying fox
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz
BLASTZ_O=400
BLASTZ_E=30
BLASTZ_M=254
# default BLASTZ_Q score matrix:
#       A     C     G     T
# A    91  -114   -31  -123
# C  -114   100  -125   -31
# G   -31  -125   100  -114
# T  -123   -31  -114    91

# TARGET: human hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CTGDIR=/hive/data/genomes/hg38/hg38.contigs.2bit
SEQ1_CTGLEN=/hive/data/genomes/hg38/hg38.contigs.chrom.sizes
SEQ1_LIFT=/hive/data/genomes/hg38/jkStuff/hg38.contigs.lift
SEQ1_CHUNK=40000000
SEQ1_LIMIT=30
SEQ1_LAP=10000

# QUERY: Black flying fox pteAle1
SEQ2_DIR=/hive/data/genomes/pteAle1/pteAle1.2bit
SEQ2_LEN=/hive/data/genomes/pteAle1/chrom.sizes
SEQ2_CHUNK=20000000
SEQ2_LIMIT=100
SEQ2_LAP=0

BASE=/hive/data/genomes/hg38/bed/lastzPteAle1.2015-04-28
TMPDIR=/dev/shm
'_EOF_'
    # << happy emacs

    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
        -chainMinScore=3000 -chainLinearGap=medium \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > do.log 2>&1
    # real    1615m3.913s

    cat fb.hg38.chainPteAle1Link.txt
    # 1472264278 bases of 3049335806 (48.281%) in intersection
    # replacing the previous tuned version:
    # 1390855083 bases of 3049335806 (45.612%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` hg38 pteAle1) > rbest.log 2>&1 &
    # real    102m6.597s

    # and for the swap:
    mkdir /hive/data/genomes/pteAle1/bed/blastz.hg38.swap
    cd /hive/data/genomes/pteAle1/bed/blastz.hg38.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/hg38/bed/lastzPteAle1.2015-04-28/DEF \
        -swap -chainMinScore=3000 -chainLinearGap=medium \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    #  real    144m41.676s

    cat fb.pteAle1.chainHg38Link.txt
    # 1383942731 bases of 1944625202 (71.168%) in intersection
    # replacing the previous tuned version:
    # 1310659904 bases of 1944625202 (67.399%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` pteAle1 hg38) > rbest.log 2>&1
    # real    51m1.756s

#########################################################################
# LASTZ human/hg38 vs. pig/susScr3 - (DONE - 2015-04-28 - Hiram)
    mkdir /hive/data/genomes/hg38/bed/lastzSusScr3.2015-04-28
    cd /hive/data/genomes/hg38/bed/lastzSusScr3.2015-04-28

    cat << '_EOF_' > DEF
# human vs pig
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz
BLASTZ_O=400
BLASTZ_E=30
BLASTZ_M=254
# default BLASTZ_Q score matrix:
#       A     C     G     T
# A    91  -114   -31  -123
# C  -114   100  -125   -31
# G   -31  -125   100  -114
# T  -123   -31  -114    91

# TARGET: human hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CTGDIR=/hive/data/genomes/hg38/hg38.contigs.2bit
SEQ1_CTGLEN=/hive/data/genomes/hg38/hg38.contigs.chrom.sizes
SEQ1_LIFT=/hive/data/genomes/hg38/jkStuff/hg38.contigs.lift
SEQ1_CHUNK=40000000
SEQ1_LIMIT=30
SEQ1_LAP=10000

# QUERY: pig susScr3
SEQ2_DIR=/hive/data/genomes/susScr3/susScr3.2bit
SEQ2_LEN=/hive/data/genomes/susScr3/chrom.sizes
SEQ2_CHUNK=20000000
SEQ2_LIMIT=30
SEQ2_LAP=0

BASE=/hive/data/genomes/hg38/bed/lastzSusScr3.2015-04-28
TMPDIR=/dev/shm
'_EOF_'
    # << happy emacs

    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
        -chainMinScore=3000 -chainLinearGap=medium \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > do.log 2>&1
    # real    1570m22.537s

    cat fb.hg38.chainSusScr3Link.txt
    # 1362333591 bases of 3049335806 (44.676%) in intersection
    # replacing the previous tuned version:
    # 1260167798 bases of 3049335806 (41.326%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` hg38 susScr3) > rbest.log 2>&1 &
    # real    49m20.123s

    # and for the swap:
    mkdir /hive/data/genomes/susScr3/bed/blastz.hg38.swap
    cd /hive/data/genomes/susScr3/bed/blastz.hg38.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/hg38/bed/lastzSusScr3.2015-04-28/DEF \
        -swap -chainMinScore=3000 -chainLinearGap=medium \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    #  real    112m33.386s

    cat fb.susScr3.chainHg38Link.txt
    # 1446310692 bases of 2525294057 (57.273%) in intersection
    # replacing the previous tuned version:
    # 1338540526 bases of 2525294057 (53.005%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` susScr3 hg38) > rbest.log 2>&1
    # real    47m22.984s

#########################################################################
# LASTZ human/hg38 vs. elephant/loxAfr3 - (DONE - 2015-04-28 - Hiram)
    mkdir /hive/data/genomes/hg38/bed/lastzLoxAfr3.2015-04-28
    cd /hive/data/genomes/hg38/bed/lastzLoxAfr3.2015-04-28

    cat << '_EOF_' > DEF
# human vs elephant
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz
BLASTZ_O=400
BLASTZ_E=30
BLASTZ_M=254
# default BLASTZ_Q score matrix:
#       A     C     G     T
# A    91  -114   -31  -123
# C  -114   100  -125   -31
# G   -31  -125   100  -114
# T  -123   -31  -114    91

# TARGET: human hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CTGDIR=/hive/data/genomes/hg38/hg38.contigs.2bit
SEQ1_CTGLEN=/hive/data/genomes/hg38/hg38.contigs.chrom.sizes
SEQ1_LIFT=/hive/data/genomes/hg38/jkStuff/hg38.contigs.lift
SEQ1_CHUNK=40000000
SEQ1_LIMIT=30
SEQ1_LAP=10000

# QUERY: elephant loxAfr3
SEQ2_DIR=/hive/data/genomes/loxAfr3/loxAfr3.2bit
SEQ2_LEN=/hive/data/genomes/loxAfr3/chrom.sizes
SEQ2_CHUNK=20000000
SEQ2_LIMIT=30
SEQ2_LAP=0

BASE=/hive/data/genomes/hg38/bed/lastzLoxAfr3.2015-04-28
TMPDIR=/dev/shm
'_EOF_'
    # << happy emacs

    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
        -chainMinScore=3000 -chainLinearGap=medium \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > do.log 2>&1
    # real    1717m57.837s


    cat fb.hg38.chainLoxAfr3Link.txt
    # 1378739469 bases of 3049335806 (45.214%) in intersection
    # replacing the previous tuned version:
    # 1277792660 bases of 3049335806 (41.904%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` hg38 loxAfr3) > rbest.log 2>&1 &
    # real    140m31.966s

    # and for the swap:
    mkdir /hive/data/genomes/loxAfr3/bed/blastz.hg38.swap
    cd /hive/data/genomes/loxAfr3/bed/blastz.hg38.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/hg38/bed/lastzLoxAfr3.2015-04-28/DEF \
        -swap -chainMinScore=3000 -chainLinearGap=medium \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    #  real    121m44.548s

    cat fb.loxAfr3.chainHg38Link.txt
    # 1319251552 bases of 3118565340 (42.303%) in intersection
    # replacing the previous tuned version:
    # 1220708619 bases of 3118565340 (39.143%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` loxAfr3 hg38) > rbest.log 2>&1
    # real    45m9.386s

#########################################################################
# LASTZ human/hg38 vs. Naked mole rat/hetGla2 - (DONE - 2015-04-28 - Hiram)
    mkdir /hive/data/genomes/hg38/bed/lastzHetGla2.2015-04-28
    cd /hive/data/genomes/hg38/bed/lastzHetGla2.2015-04-28

    cat << '_EOF_' > DEF
# human vs Naked mole rat
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz
BLASTZ_O=400
BLASTZ_E=30
BLASTZ_M=254
# default BLASTZ_Q score matrix:
#       A     C     G     T
# A    91  -114   -31  -123
# C  -114   100  -125   -31
# G   -31  -125   100  -114
# T  -123   -31  -114    91

# TARGET: human hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CTGDIR=/hive/data/genomes/hg38/hg38.contigs.2bit
SEQ1_CTGLEN=/hive/data/genomes/hg38/hg38.contigs.chrom.sizes
SEQ1_LIFT=/hive/data/genomes/hg38/jkStuff/hg38.contigs.lift
SEQ1_CHUNK=40000000
SEQ1_LIMIT=30
SEQ1_LAP=10000

# QUERY: Naked mole rat hetGla2
SEQ2_DIR=/hive/data/genomes/hetGla2/hetGla2.2bit
SEQ2_LEN=/hive/data/genomes/hetGla2/chrom.sizes
SEQ2_CHUNK=20000000
SEQ2_LIMIT=30
SEQ2_LAP=0

BASE=/hive/data/genomes/hg38/bed/lastzHetGla2.2015-04-28
TMPDIR=/dev/shm
'_EOF_'
    # << happy emacs

    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
        -chainMinScore=3000 -chainLinearGap=medium \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > do.log 2>&1
    # real    1681m38.688s

    cat fb.hg38.chainHetGla2Link.txt
    # 1410266478 bases of 3049335806 (46.248%) in intersection
    # replacing the previous tuned version:
    # 1290312728 bases of 3049335806 (42.315%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` hg38 hetGla2) > rbest.log 2>&1 &
    # real    137m40.853s

    # and for the swap:
    mkdir /hive/data/genomes/hetGla2/bed/blastz.hg38.swap
    cd /hive/data/genomes/hetGla2/bed/blastz.hg38.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/hg38/bed/lastzHetGla2.2015-04-28/DEF \
        -swap -chainMinScore=3000 -chainLinearGap=medium \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    # real    114m42.322s

    cat fb.hetGla2.chainHg38Link.txt
    # 1362365778 bases of 2314771103 (58.855%) in intersection
    # replacing the previous tuned version:
    # 1251393586 bases of 2314771103 (54.061%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` hetGla2 hg38) > rbest.log 2>&1
    # real    41m49.099s

#########################################################################
# LASTZ human/hg38 vs. megabat/pteVam1 - (DONE - 2015-04-28 - Hiram)
    mkdir /hive/data/genomes/hg38/bed/lastzPteVam1.2015-04-28
    cd /hive/data/genomes/hg38/bed/lastzPteVam1.2015-04-28

    cat << '_EOF_' > DEF
# human vs megabat
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz
BLASTZ_O=400
BLASTZ_E=30
BLASTZ_M=254
# default BLASTZ_Q score matrix:
#       A     C     G     T
# A    91  -114   -31  -123
# C  -114   100  -125   -31
# G   -31  -125   100  -114
# T  -123   -31  -114    91

# TARGET: human hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CTGDIR=/hive/data/genomes/hg38/hg38.contigs.2bit
SEQ1_CTGLEN=/hive/data/genomes/hg38/hg38.contigs.chrom.sizes
SEQ1_LIFT=/hive/data/genomes/hg38/jkStuff/hg38.contigs.lift
SEQ1_CHUNK=40000000
SEQ1_LIMIT=30
SEQ1_LAP=10000

# QUERY: megabat pteVam1
SEQ2_DIR=/hive/data/genomes/pteVam1/pteVam1.2bit
SEQ2_LEN=/hive/data/genomes/pteVam1/chrom.sizes
SEQ2_CHUNK=20000000
SEQ2_LIMIT=120
SEQ2_LAP=0

BASE=/hive/data/genomes/hg38/bed/lastzPteVam1.2015-04-28
TMPDIR=/dev/shm
'_EOF_'
    # << happy emacs

    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
        -chainMinScore=3000 -chainLinearGap=medium \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > do.log 2>&1
    # real    1499m5.523s

    cat fb.hg38.chainPteVam1Link.txt
    # 1339387555 bases of 3049335806 (43.924%) in intersection
    # replacing the previous tuned version:
    # 1250608381 bases of 3049335806 (41.012%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` hg38 pteVam1) > rbest.log 2>&1 &
    # real    33m53.542s

    # and for the swap:
    mkdir /hive/data/genomes/pteVam1/bed/blastz.hg38.swap
    cd /hive/data/genomes/pteVam1/bed/blastz.hg38.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/hg38/bed/lastzPteVam1.2015-04-28/DEF \
        -swap -chainMinScore=3000 -chainLinearGap=medium \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    #  real    135m10.167s

    cat fb.pteVam1.chainHg38Link.txt
    # 1279228346 bases of 1839436660 (69.545%) in intersection
    # replacing the previous tuned version:
    # 1198492243 bases of 1839436660 (65.155%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` pteVam1 hg38) > rbest.log 2>&1
    # real    152m29.972s

#########################################################################
# LASTZ human/hg38 vs. cat/felCat8 - (DONE - 2015-04-28 - Hiram)
    mkdir /hive/data/genomes/hg38/bed/lastzFelCat8.2015-04-28
    cd /hive/data/genomes/hg38/bed/lastzFelCat8.2015-04-28

    cat << '_EOF_' > DEF
# human vs cat
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz
BLASTZ_O=400
BLASTZ_E=30
BLASTZ_M=254
# default BLASTZ_Q score matrix:
#       A     C     G     T
# A    91  -114   -31  -123
# C  -114   100  -125   -31
# G   -31  -125   100  -114
# T  -123   -31  -114    91

# TARGET: human hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CTGDIR=/hive/data/genomes/hg38/hg38.contigs.2bit
SEQ1_CTGLEN=/hive/data/genomes/hg38/hg38.contigs.chrom.sizes
SEQ1_LIFT=/hive/data/genomes/hg38/jkStuff/hg38.contigs.lift
SEQ1_CHUNK=40000000
SEQ1_LIMIT=30
SEQ1_LAP=10000

# QUERY: cat felCat8
SEQ2_DIR=/hive/data/genomes/felCat8/felCat8.2bit
SEQ2_LEN=/hive/data/genomes/felCat8/chrom.sizes
SEQ2_CHUNK=20000000
SEQ2_LIMIT=400
SEQ2_LAP=0

BASE=/hive/data/genomes/hg38/bed/lastzFelCat8.2015-04-28
TMPDIR=/dev/shm
'_EOF_'
    # << happy emacs

    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
        -chainMinScore=3000 -chainLinearGap=medium \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > do.log 2>&1
    # real    2218m28.035s

    cat fb.hg38.chainFelCat8Link.txt
    # 1576029345 bases of 3049335806 (51.684%) in intersection
    # replacing the previous tuned version:
    # 1454517955 bases of 3049335806 (47.700%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` hg38 felCat8) > rbest.log 2>&1 &
    # real    57m53.174s

    # and for the swap:
    mkdir /hive/data/genomes/felCat8/bed/blastz.hg38.swap
    cd /hive/data/genomes/felCat8/bed/blastz.hg38.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/hg38/bed/lastzFelCat8.2015-04-28/DEF \
        -swap -chainMinScore=3000 -chainLinearGap=medium \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    #  real    300m16.338s

    cat fb.felCat8.chainHg38Link.txt
    # 1527336267 bases of 2599716822 (58.750%) in intersection
    # replacing the previous tuned version:
    # 1408124069 bases of 2599716822 (54.165%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` felCat8 hg38) \
       > rbest.log 2>&1
    # real    113m7.878s
    # finished broken recipBest run:
    # real    148m36.100s

#########################################################################
# LASTZ human/hg38 vs. panda/ailMel1 - (DONE - 2015-02-11 - Hiram)
    mkdir /hive/data/genomes/hg38/bed/lastzAilMel1.2015-02-11
    cd /hive/data/genomes/hg38/bed/lastzAilMel1.2015-02-11

# parameters obtained from a tuning run of lastz_D
# /hive/users/hiram/multiz/100way/hg38.ailMel1/hg38.ailMel1.tuning.top400.txt
    cp -p /hive/users/hiram/multiz/100way/hg38.ailMel1/hg38.ailMel1.tuning.top400.txt \
         ./hg38.ailMel1.tuning.Q.txt

    cat << '_EOF_' > DEF
# human vs panda
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.54/bin/lastz
BLASTZ_O=400
BLASTZ_E=30
BLASTZ_X=740
BLASTZ_Y=3400
BLASTZ_M=50
BLASTZ_Q=/hive/data/genomes/hg38/bed/lastzAilMel1.2015-02-11/hg38.ailMel1.tuning.Q.txt
#       A     C     G     T
# A    74  -117   -23  -133
# C  -117   100  -112   -23
# G   -23  -112   100  -117
# T  -133   -23  -117    74

# TARGET: human hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CTGDIR=/hive/data/genomes/hg38/hg38.contigs.2bit
SEQ1_CTGLEN=/hive/data/genomes/hg38/hg38.contigs.chrom.sizes
SEQ1_LIFT=/hive/data/genomes/hg38/jkStuff/hg38.contigs.lift
SEQ1_CHUNK=40000000
SEQ1_LIMIT=30
SEQ1_LAP=10000

# QUERY: panda ailMel1
SEQ2_DIR=/hive/data/genomes/ailMel1/ailMel1.2bit
SEQ2_LEN=/hive/data/genomes/ailMel1/chrom.sizes
SEQ2_CHUNK=20000000
SEQ2_LIMIT=130
SEQ2_LAP=0

BASE=/hive/data/genomes/hg38/bed/lastzAilMel1.2015-02-11
TMPDIR=/dev/shm
'_EOF_'
    # << happy emacs

    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
        -chainMinScore=3000 -chainLinearGap=medium \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > do.log 2>&1
    # real    830m30.518s

    cat fb.hg38.chainAilMel1Link.txt
    # 1470587412 bases of 3049335806 (48.226%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` hg38 ailMel1) > rbest.log 2>&1 &
    # real    34m53.243s

    # and for the swap:
    mkdir /hive/data/genomes/ailMel1/bed/blastz.hg38.swap
    cd /hive/data/genomes/ailMel1/bed/blastz.hg38.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/hg38/bed/lastzAilMel1.2015-02-11/DEF \
        -swap -chainMinScore=3000 -chainLinearGap=medium \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    #  real    88m43.119s

    cat fb.ailMel1.chainHg38Link.txt
    # 1384233285 bases of 2245312831 (61.650%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` ailMel1 hg38) > rbest.log 2>&1
    # real    41m48.012s

#########################################################################
# LASTZ human/hg38 vs. ferret/musFur1 - (DONE - 2015-04-28 - Hiram)
    mkdir /hive/data/genomes/hg38/bed/lastzMusFur1.2015-04-28
    cd /hive/data/genomes/hg38/bed/lastzMusFur1.2015-04-28

    cat << '_EOF_' > DEF
# human vs ferret
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz
BLASTZ_O=400
BLASTZ_E=30
BLASTZ_M=254
# default BLASTZ_Q score matrix:
#       A     C     G     T
# A    91  -114   -31  -123
# C  -114   100  -125   -31
# G   -31  -125   100  -114
# T  -123   -31  -114    91

# TARGET: human hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CTGDIR=/hive/data/genomes/hg38/hg38.contigs.2bit
SEQ1_CTGLEN=/hive/data/genomes/hg38/hg38.contigs.chrom.sizes
SEQ1_LIFT=/hive/data/genomes/hg38/jkStuff/hg38.contigs.lift
SEQ1_CHUNK=40000000
SEQ1_LIMIT=30
SEQ1_LAP=10000

# QUERY: ferret musFur1
SEQ2_DIR=/hive/data/genomes/musFur1/musFur1.2bit
SEQ2_LEN=/hive/data/genomes/musFur1/chrom.sizes
SEQ2_CHUNK=20000000
SEQ2_LIMIT=30
SEQ2_LAP=0

BASE=/hive/data/genomes/hg38/bed/lastzMusFur1.2015-04-28
TMPDIR=/dev/shm
'_EOF_'
    # << happy emacs

    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
        -chainMinScore=3000 -chainLinearGap=medium \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > do.log 2>&1
    # real    405m30.959s

    cat fb.hg38.chainMusFur1Link.txt
    # 1513410953 bases of 3049335806 (49.631%) in intersection
    # replacing the previous tuned version:
    # 1396051514 bases of 3049335806 (45.782%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` hg38 musFur1) > rbest.log 2>&1 &
    # real    86m22.214s

    # and for the swap:
    mkdir /hive/data/genomes/musFur1/bed/blastz.hg38.swap
    cd /hive/data/genomes/musFur1/bed/blastz.hg38.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/hg38/bed/lastzMusFur1.2015-04-28/DEF \
        -swap -chainMinScore=3000 -chainLinearGap=medium \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    #  real    103m55.044s

    cat fb.musFur1.chainHg38Link.txt
    # 1421314098 bases of 2277906570 (62.396%) in intersection
    # replacing the previous tuned version:
    # 1313363964 bases of 2277906570 (57.657%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` musFur1 hg38) > rbest.log 2>&1
    # real    40m15.023s

#########################################################################
# LASTZ human/hg38 vs. guinea pig/cavPor3 - (DONE - 2015-04-27 - Hiram)
    mkdir /hive/data/genomes/hg38/bed/lastzCavPor3.2015-04-27
    cd /hive/data/genomes/hg38/bed/lastzCavPor3.2015-04-27

    cat << '_EOF_' > DEF
# human vs guinea pig
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz
BLASTZ_O=400
BLASTZ_E=30
BLASTZ_M=254
# default BLASTZ_Q score matrix:
#       A     C     G     T
# A    91  -114   -31  -123
# C  -114   100  -125   -31
# G   -31  -125   100  -114
# T  -123   -31  -114    91

# TARGET: human hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CTGDIR=/hive/data/genomes/hg38/hg38.contigs.2bit
SEQ1_CTGLEN=/hive/data/genomes/hg38/hg38.contigs.chrom.sizes
SEQ1_LIFT=/hive/data/genomes/hg38/jkStuff/hg38.contigs.lift
SEQ1_CHUNK=40000000
SEQ1_LIMIT=30
SEQ1_LAP=10000

# QUERY: guinea pig cavPor3
SEQ2_DIR=/hive/data/genomes/cavPor3/cavPor3.2bit
SEQ2_LEN=/hive/data/genomes/cavPor3/chrom.sizes
SEQ2_CHUNK=20000000
SEQ2_LIMIT=20
SEQ2_LAP=0

BASE=/hive/data/genomes/hg38/bed/lastzCavPor3.2015-04-27
TMPDIR=/dev/shm
'_EOF_'
    # << happy emacs

    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
        -chainMinScore=3000 -chainLinearGap=medium \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > do.log 2>&1
    # real    1456m13.633s

    cat fb.hg38.chainCavPor3Link.txt
    # 1292035815 bases of 3049335806 (42.371%) in intersection
    # replacing the previous tuned version:
    # 1155740911 bases of 3049335806 (37.901%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` hg38 cavPor3) > rbest.log 2>&1 &
    # real    40m47.501s

    # and for the swap:
    mkdir /hive/data/genomes/cavPor3/bed/blastz.hg38.swap
    cd /hive/data/genomes/cavPor3/bed/blastz.hg38.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/hg38/bed/lastzCavPor3.2015-04-27/DEF \
        -swap -chainMinScore=3000 -chainLinearGap=medium \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    #  real    147m52.206s

    cat fb.cavPor3.chainHg38Link.txt
    # 1278427131 bases of 2663369733 (48.000%) in intersection
    # replacing the previous tuned version:
    # 1142636457 bases of 2663369733 (42.902%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` cavPor3 hg38) > rbest.log 2>&1
    # real    132m10.182s

#########################################################################
# LASTZ human/hg38 vs. armadillo/dasNov3 - (DONE - 2015-04-28 - Hiram)
    mkdir /hive/data/genomes/hg38/bed/lastzDasNov3.2015-04-28
    cd /hive/data/genomes/hg38/bed/lastzDasNov3.2015-04-28

    cat << '_EOF_' > DEF
# human vs armadillo
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz
BLASTZ_O=400
BLASTZ_E=30
BLASTZ_M=254
# default BLASTZ_Q score matrix:
#       A     C     G     T
# A    91  -114   -31  -123
# C  -114   100  -125   -31
# G   -31  -125   100  -114
# T  -123   -31  -114    91

# TARGET: human hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CTGDIR=/hive/data/genomes/hg38/hg38.contigs.2bit
SEQ1_CTGLEN=/hive/data/genomes/hg38/hg38.contigs.chrom.sizes
SEQ1_LIFT=/hive/data/genomes/hg38/jkStuff/hg38.contigs.lift
SEQ1_CHUNK=40000000
SEQ1_LIMIT=30
SEQ1_LAP=10000

# QUERY: armadillo dasNov3
SEQ2_DIR=/hive/data/genomes/dasNov3/dasNov3.2bit
SEQ2_LEN=/hive/data/genomes/dasNov3/chrom.sizes
SEQ2_CHUNK=20000000
SEQ2_LIMIT=80
SEQ2_LAP=0

BASE=/hive/data/genomes/hg38/bed/lastzDasNov3.2015-04-28
TMPDIR=/dev/shm
'_EOF_'
    # << happy emacs

    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
        -chainMinScore=3000 -chainLinearGap=medium \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > do.log 2>&1
    # real    1719m25.419s

    cat fb.hg38.chainDasNov3Link.txt
    # 1382853067 bases of 3049335806 (45.349%) in intersection
    # replacing the previous tuned version:
    # 1287831558 bases of 3049335806 (42.233%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` hg38 dasNov3) > rbest.log 2>&1 &
    # real    491m51.020s

    # load up the recip best chainNet tables
    time (doRecipBest.pl -load -continue=load -workhorse=hgwdev \
	-buildDir=`pwd` hg38 dasNov3) > loadRBest.log 2>&1 &
    # real    12m39.283s

    cat fb.hg38.chainRBestDasNov3Link.txt
    # 1267819323 bases of 3049335806 (41.577%) in intersection

    # create and load up the syntenic chainNet tables 2017-10-30
cd /hive/data/genomes/hg38/bed/lastzDasNov3.2015-04-28/axtChain
netToAxt hg38.dasNov3.syn.net.gz hg38.dasNov3.all.chain.gz \
/scratch/data/hg38/hg38.2bit /hive/data/genomes/dasNov3/dasNov3.2bit stdout \
  | axtSort stdin stdout \
     | axtToChain stdin /hive/data/genomes/hg38/chrom.sizes \
        /hive/data/genomes/dasNov3/chrom.sizes stdout \
            | gzip -c > hg38.dasNov3.syn.chain.gz
hgLoadChain -tIndex hg38 chainSynDasNov3 hg38.dasNov3.syn.chain.gz
netFilter -minGap=10 hg38.dasNov3.syn.net.gz \
  | hgLoadNet -verbose=0 hg38 netSynDasNov3 stdin
cd /hive/data/genomes/hg38/bed/lastzDasNov3.2015-04-28
featureBits hg38 chainSynDasNov3Link > fb.hg38.chainSynDasNov3Link.txt 2>&1
cat fb.hg38.chainSynDasNov3Link.txt
# 1302517110 bases of 3049335806 (42.715%) in intersection


    # and for the swap:
    mkdir /hive/data/genomes/dasNov3/bed/blastz.hg38.swap
    cd /hive/data/genomes/dasNov3/bed/blastz.hg38.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/hg38/bed/lastzDasNov3.2015-04-28/DEF \
        -swap -chainMinScore=3000 -chainLinearGap=medium \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    # real    139m24.821s

    cat fb.dasNov3.chainHg38Link.txt
    # 1382479617 bases of 3299882059 (41.895%) in intersection
    # replacing the previous tuned version:
    # 1284164290 bases of 3299882059 (38.915%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` dasNov3 hg38) > rbest.log 2>&1
    # real    78m34.471s

#########################################################################
# LASTZ human/hg38 vs. rabbit/oryCun2 - (DONE - 2015-04-27 - Hiram)
    mkdir /hive/data/genomes/hg38/bed/lastzOryCun2.2015-04-27
    cd /hive/data/genomes/hg38/bed/lastzOryCun2.2015-04-27

    cat << '_EOF_' > DEF
# human vs rabbit
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz
BLASTZ_O=400
BLASTZ_E=30
BLASTZ_M=254
# default BLASTZ_Q score matrix:
#       A     C     G     T
# A    91  -114   -31  -123
# C  -114   100  -125   -31
# G   -31  -125   100  -114
# T  -123   -31  -114    91

# TARGET: human hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CTGDIR=/hive/data/genomes/hg38/hg38.contigs.2bit
SEQ1_CTGLEN=/hive/data/genomes/hg38/hg38.contigs.chrom.sizes
SEQ1_LIFT=/hive/data/genomes/hg38/jkStuff/hg38.contigs.lift
SEQ1_CHUNK=40000000
SEQ1_LIMIT=30
SEQ1_LAP=10000

# QUERY: rabbit oryCun2
SEQ2_DIR=/hive/data/genomes/oryCun2/oryCun2.2bit
SEQ2_LEN=/hive/data/genomes/oryCun2/chrom.sizes
SEQ2_CHUNK=20000000
SEQ2_LIMIT=10
SEQ2_LAP=0

BASE=/hive/data/genomes/hg38/bed/lastzOryCun2.2015-04-27
TMPDIR=/dev/shm
'_EOF_'
    # << happy emacs

    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
        -chainMinScore=3000 -chainLinearGap=medium \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > do.log 2>&1
    # real    1143m17.631s

    cat fb.hg38.chainOryCun2Link.txt
    # 1308502981 bases of 3049335806 (42.911%) in intersection
    # replacing the previous tuned version:
    # 1177978746 bases of 3049335806 (38.631%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` hg38 oryCun2) > rbest.log 2>&1 &
    # real    39m0.464s

    # and for the swap:
    mkdir /hive/data/genomes/oryCun2/bed/blastz.hg38.swap
    cd /hive/data/genomes/oryCun2/bed/blastz.hg38.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/hg38/bed/lastzOryCun2.2015-04-27/DEF \
        -swap -chainMinScore=3000 -chainLinearGap=medium \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    #  real    107m40.781s

    cat fb.oryCun2.chainHg38Link.txt
    # 1259317035 bases of 2604023284 (48.360%) in intersection
    # replacing the previous tuned version:
    # 1136478377 bases of 2604023284 (43.643%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` oryCun2 hg38) > rbest.log 2>&1
    # real    74m17.119s

#########################################################################
# LASTZ human/hg38 vs. Tibetan antelope/panHod1 - (DONE - 2015-04-27 - Hiram)
    mkdir /hive/data/genomes/hg38/bed/lastzPanHod1.2015-04-27
    cd /hive/data/genomes/hg38/bed/lastzPanHod1.2015-04-27

    cat << '_EOF_' > DEF
# human vs Tibetan antelope
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz
BLASTZ_O=400
BLASTZ_E=30
BLASTZ_M=254
# default BLASTZ_Q score matrix:
#       A     C     G     T
# A    91  -114   -31  -123
# C  -114   100  -125   -31
# G   -31  -125   100  -114
# T  -123   -31  -114    91

# TARGET: human hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CTGDIR=/hive/data/genomes/hg38/hg38.contigs.2bit
SEQ1_CTGLEN=/hive/data/genomes/hg38/hg38.contigs.chrom.sizes
SEQ1_LIFT=/hive/data/genomes/hg38/jkStuff/hg38.contigs.lift
SEQ1_CHUNK=40000000
SEQ1_LIMIT=30
SEQ1_LAP=10000

# QUERY: Tibetan antelope panHod1
SEQ2_DIR=/hive/data/genomes/panHod1/panHod1.2bit
SEQ2_LEN=/hive/data/genomes/panHod1/chrom.sizes
SEQ2_CHUNK=20000000
SEQ2_LIMIT=30
SEQ2_LAP=0

BASE=/hive/data/genomes/hg38/bed/lastzPanHod1.2015-04-27
TMPDIR=/dev/shm
'_EOF_'
    # << happy emacs

    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
        -chainMinScore=3000 -chainLinearGap=medium \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > do.log 2>&1
    # real    1194m17.831s

    cat fb.hg38.chainPanHod1Link.txt
    # 1391091506 bases of 3049335806 (45.619%) in intersection
    # replacing the previous tuned version:
    # 1261119369 bases of 3049335806 (41.357%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` hg38 panHod1) > rbest.log 2>&1 &
    # real    84m43.209s

    # and for the swap:
    mkdir /hive/data/genomes/panHod1/bed/blastz.hg38.swap
    cd /hive/data/genomes/panHod1/bed/blastz.hg38.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/hg38/bed/lastzPanHod1.2015-04-27/DEF \
        -swap -chainMinScore=3000 -chainLinearGap=medium \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    #  real    112m26.689s

    cat fb.panHod1.chainHg38Link.txt
    # 1317338279 bases of 2507986438 (52.526%) in intersection
    # replacing the previous tuned version:
    # 1196606934 bases of 2507986438 (47.712%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` panHod1 hg38) > rbest.log 2>&1
    # real    441m32.946s finished manually real    53m30.864s
    time (doRecipBest.pl -workhorse=hgwdev -continue=download \
      -buildDir=`pwd` panHod1 hg38) > rbestDownload.log 2>&1
    # real    0m4.397s

#########################################################################
# LASTZ human/hg38 vs. Weddell seal/lepWed1 - (DONE - 2015-04-28 - Hiram)
    mkdir /hive/data/genomes/hg38/bed/lastzLepWed1.2015-04-28
    cd /hive/data/genomes/hg38/bed/lastzLepWed1.2015-04-28

    cat << '_EOF_' > DEF
# human vs Weddell seal
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz
BLASTZ_O=400
BLASTZ_E=30
BLASTZ_M=254
# default BLASTZ_Q score matrix:
#       A     C     G     T
# A    91  -114   -31  -123
# C  -114   100  -125   -31
# G   -31  -125   100  -114
# T  -123   -31  -114    91

# TARGET: human hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CTGDIR=/hive/data/genomes/hg38/hg38.contigs.2bit
SEQ1_CTGLEN=/hive/data/genomes/hg38/hg38.contigs.chrom.sizes
SEQ1_LIFT=/hive/data/genomes/hg38/jkStuff/hg38.contigs.lift
SEQ1_CHUNK=40000000
SEQ1_LIMIT=30
SEQ1_LAP=10000

# QUERY: Weddell seal lepWed1
SEQ2_DIR=/hive/data/genomes/lepWed1/lepWed1.2bit
SEQ2_LEN=/hive/data/genomes/lepWed1/chrom.sizes
SEQ2_CHUNK=20000000
SEQ2_LIMIT=30
SEQ2_LAP=0

BASE=/hive/data/genomes/hg38/bed/lastzLepWed1.2015-04-28
TMPDIR=/dev/shm
'_EOF_'
    # << happy emacs

    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
        -chainMinScore=3000 -chainLinearGap=medium \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > do.log 2>&1
    # real    1527m39.249s

    cat fb.hg38.chainLepWed1Link.txt
    # 1557394982 bases of 3049335806 (51.073%) in intersection
    # replacing the previous tuned version:
    # 1446510291 bases of 3049335806 (47.437%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` hg38 lepWed1) > rbest.log 2>&1 &
    # real    70m0.849s

    # and for the swap:
    mkdir /hive/data/genomes/lepWed1/bed/blastz.hg38.swap
    cd /hive/data/genomes/lepWed1/bed/blastz.hg38.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/hg38/bed/lastzLepWed1.2015-04-28/DEF \
        -swap -chainMinScore=3000 -chainLinearGap=medium \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    #  real    112m55.510s

    cat fb.lepWed1.chainHg38Link.txt
    # 1459320253 bases of 2223164129 (65.642%) in intersection
    # replacing the previous tuned version:
    # 1358644851 bases of 2223164129 (61.113%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` lepWed1 hg38) > rbest.log 2>&1
    # real    83m25.807s

#########################################################################
# LASTZ human/hg38 vs. Pacific walrus/odoRosDiv1 - (DONE - 2015-04-28 - Hiram)
    mkdir /hive/data/genomes/hg38/bed/lastzOdoRosDiv1.2015-04-28
    cd /hive/data/genomes/hg38/bed/lastzOdoRosDiv1.2015-04-28

    cat << '_EOF_' > DEF
# human vs Pacific walrus
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz
BLASTZ_O=400
BLASTZ_E=30
BLASTZ_M=254
# default BLASTZ_Q score matrix:
#       A     C     G     T
# A    91  -114   -31  -123
# C  -114   100  -125   -31
# G   -31  -125   100  -114
# T  -123   -31  -114    91

# TARGET: human hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CTGDIR=/hive/data/genomes/hg38/hg38.contigs.2bit
SEQ1_CTGLEN=/hive/data/genomes/hg38/hg38.contigs.chrom.sizes
SEQ1_LIFT=/hive/data/genomes/hg38/jkStuff/hg38.contigs.lift
SEQ1_CHUNK=40000000
SEQ1_LIMIT=30
SEQ1_LAP=10000

# QUERY: Pacific walrus odoRosDiv1
SEQ2_DIR=/hive/data/genomes/odoRosDiv1/odoRosDiv1.2bit
SEQ2_LEN=/hive/data/genomes/odoRosDiv1/chrom.sizes
SEQ2_CHUNK=20000000
SEQ2_LIMIT=10
SEQ2_LAP=0

BASE=/hive/data/genomes/hg38/bed/lastzOdoRosDiv1.2015-04-28
TMPDIR=/dev/shm
'_EOF_'
    # << happy emacs

    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
        -chainMinScore=3000 -chainLinearGap=medium \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -noDbNameCheck -syntenicNet) > do.log 2>&1
    # real    1559m56.509s

    cat fb.hg38.chainOdoRosDiv1Link.txt
    # 1591525110 bases of 3049335806 (52.193%) in intersection
    # replacing the previous tuned version:
    # 1463226456 bases of 3049335806 (47.985%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` hg38 odoRosDiv1) > rbest.log 2>&1 &
    # real    68m19.885s

    # and for the swap:
    mkdir /hive/data/genomes/odoRosDiv1/bed/blastz.hg38.swap
    cd /hive/data/genomes/odoRosDiv1/bed/blastz.hg38.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/hg38/bed/lastzOdoRosDiv1.2015-04-28/DEF \
        -swap -chainMinScore=3000 -chainLinearGap=medium \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -noDbNameCheck -syntenicNet) > swap.log 2>&1
    #  real    116m42.765s

    cat fb.odoRosDiv1.chainHg38Link.txt
    # 1492793949 bases of 2300235512 (64.897%) in intersection
    # replacing the previous tuned version:
    # 1376881973 bases of 2300235512 (59.858%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` odoRosDiv1 hg38) > rbest.log 2>&1
    # real    129m15.182s

#########################################################################
# LASTZ human/hg38 vs. David's myotis bat/myoDav1 - (DONE - 2015-04-27 - Hiram)
    mkdir /hive/data/genomes/hg38/bed/lastzMyoDav1.2015-04-27
    cd /hive/data/genomes/hg38/bed/lastzMyoDav1.2015-04-27

    cat << '_EOF_' > DEF
# human vs David's myotis bat
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz
BLASTZ_O=400
BLASTZ_E=30
BLASTZ_M=254
# default BLASTZ_Q score matrix:
#       A     C     G     T
# A    91  -114   -31  -123
# C  -114   100  -125   -31
# G   -31  -125   100  -114
# T  -123   -31  -114    91

# TARGET: human hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CTGDIR=/hive/data/genomes/hg38/hg38.contigs.2bit
SEQ1_CTGLEN=/hive/data/genomes/hg38/hg38.contigs.chrom.sizes
SEQ1_LIFT=/hive/data/genomes/hg38/jkStuff/hg38.contigs.lift
SEQ1_CHUNK=40000000
SEQ1_LIMIT=30
SEQ1_LAP=10000

# QUERY: David's myotis bat myoDav1
SEQ2_DIR=/hive/data/genomes/myoDav1/myoDav1.2bit
SEQ2_LEN=/hive/data/genomes/myoDav1/chrom.sizes
SEQ2_CHUNK=20000000
SEQ2_LIMIT=150
SEQ2_LAP=0

BASE=/hive/data/genomes/hg38/bed/lastzMyoDav1.2015-04-27
TMPDIR=/dev/shm
'_EOF_'
    # << happy emacs

    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
        -chainMinScore=3000 -chainLinearGap=medium \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > do.log 2>&1
    # real    1191m1.115s

    cat fb.hg38.chainMyoDav1Link.txt
    # 1180503256 bases of 3049335806 (38.713%) in intersection
    # replacing the previous tuned version:
    # 1063972348 bases of 3049335806 (34.892%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` hg38 myoDav1) > rbest.log 2>&1 &
    # real    38m14.019s

    # and for the swap:
    mkdir /hive/data/genomes/myoDav1/bed/blastz.hg38.swap
    cd /hive/data/genomes/myoDav1/bed/blastz.hg38.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/hg38/bed/lastzMyoDav1.2015-04-27/DEF \
        -swap -chainMinScore=3000 -chainLinearGap=medium \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    #  real    122m57.687s

    cat fb.myoDav1.chainHg38Link.txt
    # 1132451816 bases of 1878461987 (60.286%) in intersection
    # replacing the previous tuned version:
    # 1025255929 bases of 1878461987 (54.580%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` myoDav1 hg38) > rbest.log 2>&1
    # real    77m7.749s

#########################################################################
# LASTZ human/hg38 vs. goat/capHir1 - (DONE - 2015-04-27 - Hiram)
    mkdir /hive/data/genomes/hg38/bed/lastzCapHir1.2015-04-27
    cd /hive/data/genomes/hg38/bed/lastzCapHir1.2015-04-27

    cat << '_EOF_' > DEF
# human vs goat
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz
BLASTZ_O=400
BLASTZ_E=30
BLASTZ_M=254
# default BLASTZ_Q score matrix:
#       A     C     G     T
# A    91  -114   -31  -123
# C  -114   100  -125   -31
# G   -31  -125   100  -114
# T  -123   -31  -114    91

# TARGET: human hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CTGDIR=/hive/data/genomes/hg38/hg38.contigs.2bit
SEQ1_CTGLEN=/hive/data/genomes/hg38/hg38.contigs.chrom.sizes
SEQ1_LIFT=/hive/data/genomes/hg38/jkStuff/hg38.contigs.lift
SEQ1_CHUNK=40000000
SEQ1_LIMIT=30
SEQ1_LAP=10000

# QUERY: goat capHir1
SEQ2_DIR=/hive/data/genomes/capHir1/capHir1.2bit
SEQ2_LEN=/hive/data/genomes/capHir1/chrom.sizes
SEQ2_CHUNK=20000000
SEQ2_LIMIT=130
SEQ2_LAP=0

BASE=/hive/data/genomes/hg38/bed/lastzCapHir1.2015-04-27
TMPDIR=/dev/shm
'_EOF_'
    # << happy emacs

    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
        -chainMinScore=3000 -chainLinearGap=medium \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > do.log 2>&1
    # real    1473m2.628s

    cat fb.hg38.chainCapHir1Link.txt
    # 1380028096 bases of 3049335806 (45.257%) in intersection
    # replacing the previous tuned version:
    # 1259921542 bases of 3049335806 (41.318%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` hg38 capHir1) > rbest.log 2>&1 &
    # real    84m49.153s

    # and for the swap:
    mkdir /hive/data/genomes/capHir1/bed/blastz.hg38.swap
    cd /hive/data/genomes/capHir1/bed/blastz.hg38.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/hg38/bed/lastzCapHir1.2015-04-27/DEF \
        -swap -chainMinScore=3000 -chainLinearGap=medium \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    #  real    128m13.474s

    cat fb.capHir1.chainHg38Link.txt
    # 1314558467 bases of 2495939845 (52.668%) in intersection
    # replacing the previous tuned version:
    # 1201106945 bases of 2495939845 (48.122%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` capHir1 hg38) > rbest.log 2>&1
    # real    432m43.547s finished manually real    65m19.641s
    time (doRecipBest.pl -workhorse=hgwdev -continue=download \
       -buildDir=`pwd` capHir1 hg38) > rbestDownload.log 2>&1
    # real    0m4.386s

#########################################################################
# LASTZ human/hg38 vs. microbat/myoLuc2 - (DONE - 2015-04-27 - Hiram)
    mkdir /hive/data/genomes/hg38/bed/lastzMyoLuc2.2015-04-27
    cd /hive/data/genomes/hg38/bed/lastzMyoLuc2.2015-04-27

    cat << '_EOF_' > DEF
# human vs microbat
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz
BLASTZ_O=400
BLASTZ_E=30
BLASTZ_M=254
# default BLASTZ_Q score matrix:
#       A     C     G     T
# A    91  -114   -31  -123
# C  -114   100  -125   -31
# G   -31  -125   100  -114
# T  -123   -31  -114    91

# TARGET: human hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CTGDIR=/hive/data/genomes/hg38/hg38.contigs.2bit
SEQ1_CTGLEN=/hive/data/genomes/hg38/hg38.contigs.chrom.sizes
SEQ1_LIFT=/hive/data/genomes/hg38/jkStuff/hg38.contigs.lift
SEQ1_CHUNK=40000000
SEQ1_LIMIT=30
SEQ1_LAP=10000

# QUERY: microbat myoLuc2
SEQ2_DIR=/hive/data/genomes/myoLuc2/myoLuc2.2bit
SEQ2_LEN=/hive/data/genomes/myoLuc2/chrom.sizes
SEQ2_CHUNK=20000000
SEQ2_LIMIT=30
SEQ2_LAP=0

BASE=/hive/data/genomes/hg38/bed/lastzMyoLuc2.2015-04-27
TMPDIR=/dev/shm
'_EOF_'
    # << happy emacs

    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
        -chainMinScore=3000 -chainLinearGap=medium \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > do.log 2>&1
    # real    1062m31.557s

    cat fb.hg38.chainMyoLuc2Link.txt
    # 1176781597 bases of 3049335806 (38.591%) in intersection
    # replacing the previous tuned version:
    # 1071766600 bases of 3049335806 (35.148%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` hg38 myoLuc2) > rbest.log 2>&1 &
    # real    31m49.720s

    # and for the swap:
    mkdir /hive/data/genomes/myoLuc2/bed/blastz.hg38.swap
    cd /hive/data/genomes/myoLuc2/bed/blastz.hg38.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/hg38/bed/lastzMyoLuc2.2015-04-27/DEF \
        -swap -chainMinScore=3000 -chainLinearGap=medium \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    #  real    101m34.047s

    cat fb.myoLuc2.chainHg38Link.txt
    # 1174515059 bases of 1966419868 (59.729%) in intersection
    # replacing the previous tuned version:
    # 1075118724 bases of 1966419868 (54.674%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` myoLuc2 hg38) > rbest.log 2>&1
    # real    103m44.974s

#########################################################################
# LASTZ human/hg38 vs. Cape elephant shrew/eleEdw1 - (DONE - 2015-02-17 - Hiram)
    mkdir /hive/data/genomes/hg38/bed/lastzEleEdw1.2015-02-17
    cd /hive/data/genomes/hg38/bed/lastzEleEdw1.2015-02-17

    cat << '_EOF_' > DEF
# human vs Cape elephant shrew
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.54/bin/lastz
BLASTZ_O=400
BLASTZ_E=30

# TARGET: human hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CTGDIR=/hive/data/genomes/hg38/hg38.contigs.2bit
SEQ1_CTGLEN=/hive/data/genomes/hg38/hg38.contigs.chrom.sizes
SEQ1_LIFT=/hive/data/genomes/hg38/jkStuff/hg38.contigs.lift
SEQ1_CHUNK=40000000
SEQ1_LIMIT=30
SEQ1_LAP=10000

# QUERY: Cape elephant shrew eleEdw1
SEQ2_DIR=/hive/data/genomes/eleEdw1/eleEdw1.2bit
SEQ2_LEN=/hive/data/genomes/eleEdw1/chrom.sizes
SEQ2_CHUNK=20000000
SEQ2_LIMIT=30
SEQ2_LAP=0

BASE=/hive/data/genomes/hg38/bed/lastzEleEdw1.2015-02-17
TMPDIR=/dev/shm
'_EOF_'
    # << happy emacs

    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
        -chainMinScore=3000 -chainLinearGap=medium \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > do.log 2>&1
    # real    2714m54.678s

    cat fb.hg38.chainEleEdw1Link.txt
    # 818423001 bases of 3049335806 (26.839%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` hg38 eleEdw1) \
       > rbest.log 2>&1 &
    # real    46m7.480s

    # and for the swap:
    mkdir /hive/data/genomes/eleEdw1/bed/blastz.hg38.swap
    cd /hive/data/genomes/eleEdw1/bed/blastz.hg38.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/hg38/bed/lastzEleEdw1.2015-02-17/DEF \
        -swap -chainMinScore=3000 -chainLinearGap=medium \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    #  real    81m53.808s

    cat fb.eleEdw1.chainHg38Link.txt
    # 801797017 bases of 3315871847 (24.181%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` eleEdw1 hg38) > rbest.log 2>&1
    # real    30m17.282s

#########################################################################
# LASTZ human/hg38 vs. manatee/triMan1 - (DONE - 2015-04-28 - Hiram)
    mkdir /hive/data/genomes/hg38/bed/lastzTriMan1.2015-04-28
    cd /hive/data/genomes/hg38/bed/lastzTriMan1.2015-04-28

    cat << '_EOF_' > DEF
# human vs manatee
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz
BLASTZ_O=400
BLASTZ_E=30
BLASTZ_M=254
# default BLASTZ_Q score matrix:
#       A     C     G     T
# A    91  -114   -31  -123
# C  -114   100  -125   -31
# G   -31  -125   100  -114
# T  -123   -31  -114    91

# TARGET: human hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CTGDIR=/hive/data/genomes/hg38/hg38.contigs.2bit
SEQ1_CTGLEN=/hive/data/genomes/hg38/hg38.contigs.chrom.sizes
SEQ1_LIFT=/hive/data/genomes/hg38/jkStuff/hg38.contigs.lift
SEQ1_CHUNK=40000000
SEQ1_LIMIT=30
SEQ1_LAP=10000

# QUERY: manatee triMan1
SEQ2_DIR=/hive/data/genomes/triMan1/triMan1.2bit
SEQ2_LEN=/hive/data/genomes/triMan1/chrom.sizes
SEQ2_CHUNK=20000000
SEQ2_LIMIT=30
SEQ2_LAP=0

BASE=/hive/data/genomes/hg38/bed/lastzTriMan1.2015-04-28
TMPDIR=/dev/shm
'_EOF_'
    # << happy emacs

    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
        -chainMinScore=3000 -chainLinearGap=medium \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > do.log 2>&1
    # real    1801m7.775s

    cat fb.hg38.chainTriMan1Link.txt
    # 1382747603 bases of 3049335806 (45.346%) in intersection
    # replacing the previous tuned version:
    # 1263723305 bases of 3049335806 (41.443%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` hg38 triMan1) > rbest.log 2>&1 &
    # real    73m5.269s

    # and for the swap:
    mkdir /hive/data/genomes/triMan1/bed/blastz.hg38.swap
    cd /hive/data/genomes/triMan1/bed/blastz.hg38.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/hg38/bed/lastzTriMan1.2015-04-28/DEF \
        -swap -chainMinScore=3000 -chainLinearGap=medium \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    #  real    103m30.816s

    cat fb.triMan1.chainHg38Link.txt
    # 1299790980 bases of 2769099677 (46.939%) in intersection
    # replacing the previous tuned version:
    # 1188634635 bases of 2769099677 (42.925%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` triMan1 hg38) \
       > rbest.log 2>&1
    # real    53m44.429s

#########################################################################
# LASTZ human/hg38 vs. lesser Egyptian jerboa/jacJac1 - (DONE - 2015-02-17 - Hiram)
    mkdir /hive/data/genomes/hg38/bed/lastzJacJac1.2015-02-17
    cd /hive/data/genomes/hg38/bed/lastzJacJac1.2015-02-17

    cat << '_EOF_' > DEF
# human vs lesser Egyptian jerboa
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.54/bin/lastz
BLASTZ_O=400
BLASTZ_E=30

# TARGET: human hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CTGDIR=/hive/data/genomes/hg38/hg38.contigs.2bit
SEQ1_CTGLEN=/hive/data/genomes/hg38/hg38.contigs.chrom.sizes
SEQ1_LIFT=/hive/data/genomes/hg38/jkStuff/hg38.contigs.lift
SEQ1_CHUNK=40000000
SEQ1_LIMIT=30
SEQ1_LAP=10000

# QUERY: lesser Egyptian jerboa jacJac1
SEQ2_DIR=/hive/data/genomes/jacJac1/jacJac1.2bit
SEQ2_LEN=/hive/data/genomes/jacJac1/chrom.sizes
SEQ2_CHUNK=20000000
SEQ2_LIMIT=30
SEQ2_LAP=0

BASE=/hive/data/genomes/hg38/bed/lastzJacJac1.2015-02-17
TMPDIR=/dev/shm
'_EOF_'
    # << happy emacs

    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
        -chainMinScore=3000 -chainLinearGap=medium \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > do.log 2>&1
    # real    3282m33.094s

    cat fb.hg38.chainJacJac1Link.txt
    # 1041439402 bases of 3049335806 (34.153%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` hg38 jacJac1) \
       > rbest.log 2>&1 &
    # real    43m41.722s

    # and for the swap:
    mkdir /hive/data/genomes/jacJac1/bed/blastz.hg38.swap
    cd /hive/data/genomes/jacJac1/bed/blastz.hg38.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/hg38/bed/lastzJacJac1.2015-02-17/DEF \
        -swap -chainMinScore=3000 -chainLinearGap=medium \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    #  real    88m19.593s

    cat fb.jacJac1.chainHg38Link.txt
    # 995506956 bases of 2470259869 (40.300%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` jacJac1 hg38) \
       > rbest.log 2>&1
    # real    46m52.984s

#########################################################################
# LASTZ human/hg38 vs. chinchilla/chiLan1 - (DONE - 2015-04-27 - Hiram)
    mkdir /hive/data/genomes/hg38/bed/lastzChiLan1.2015-04-27
    cd /hive/data/genomes/hg38/bed/lastzChiLan1.2015-04-27

    cat << '_EOF_' > DEF
# human vs chinchilla
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz
BLASTZ_O=400
BLASTZ_E=30
BLASTZ_M=254
# default BLASTZ_Q score matrix:
#       A     C     G     T
# A    91  -114   -31  -123
# C  -114   100  -125   -31
# G   -31  -125   100  -114
# T  -123   -31  -114    91

# TARGET: human hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CTGDIR=/hive/data/genomes/hg38/hg38.contigs.2bit
SEQ1_CTGLEN=/hive/data/genomes/hg38/hg38.contigs.chrom.sizes
SEQ1_LIFT=/hive/data/genomes/hg38/jkStuff/hg38.contigs.lift
SEQ1_CHUNK=40000000
SEQ1_LIMIT=30
SEQ1_LAP=10000

# QUERY: chinchilla chiLan1
SEQ2_DIR=/hive/data/genomes/chiLan1/chiLan1.2bit
SEQ2_LEN=/hive/data/genomes/chiLan1/chrom.sizes
SEQ2_CHUNK=20000000
SEQ2_LIMIT=30
SEQ2_LAP=0

BASE=/hive/data/genomes/hg38/bed/lastzChiLan1.2015-04-27
TMPDIR=/dev/shm
'_EOF_'
    # << happy emacs

    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
        -chainMinScore=3000 -chainLinearGap=medium \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > do.log 2>&1
    # real    1099m27.880s

    cat fb.hg38.chainChiLan1Link.txt
    # 1392476369 bases of 3049335806 (45.665%) in intersection
    # replacing the previous tuned version:
    # 1244377852 bases of 3049335806 (40.808%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` hg38 chiLan1) > rbest.log 2>&1 &
    # real    38m31.373s

    # and for the swap:
    mkdir /hive/data/genomes/chiLan1/bed/blastz.hg38.swap
    cd /hive/data/genomes/chiLan1/bed/blastz.hg38.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/hg38/bed/lastzChiLan1.2015-04-27/DEF \
        -swap -chainMinScore=3000 -chainLinearGap=medium \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    #  real    107m42.158s

    cat fb.chiLan1.chainHg38Link.txt
    # 1324935425 bases of 2284276400 (58.002%) in intersection
    # replacing the previous tuned version:
    # 1188638834 bases of 2284276400 (52.036%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` chiLan1 hg38) > rbest.log 2>&1
    # real    62m47.881s

#########################################################################
# LASTZ human/hg38 vs. star nosed mole/conCri1 - (DONE - 2015-04-28 - Hiram)
    mkdir /hive/data/genomes/hg38/bed/lastzConCri1.2015-04-28
    cd /hive/data/genomes/hg38/bed/lastzConCri1.2015-04-28

    cat << '_EOF_' > DEF
# human vs star nosed mole
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz
BLASTZ_O=400
BLASTZ_E=30
BLASTZ_M=254
# default BLASTZ_Q score matrix:
#       A     C     G     T
# A    91  -114   -31  -123
# C  -114   100  -125   -31
# G   -31  -125   100  -114
# T  -123   -31  -114    91

# TARGET: human hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CTGDIR=/hive/data/genomes/hg38/hg38.contigs.2bit
SEQ1_CTGLEN=/hive/data/genomes/hg38/hg38.contigs.chrom.sizes
SEQ1_LIFT=/hive/data/genomes/hg38/jkStuff/hg38.contigs.lift
SEQ1_CHUNK=40000000
SEQ1_LIMIT=30
SEQ1_LAP=10000

# QUERY: star nosed mole conCri1
SEQ2_DIR=/hive/data/genomes/conCri1/conCri1.2bit
SEQ2_LEN=/hive/data/genomes/conCri1/chrom.sizes
SEQ2_CHUNK=20000000
SEQ2_LIMIT=30
SEQ2_LAP=0

BASE=/hive/data/genomes/hg38/bed/lastzConCri1.2015-04-28
TMPDIR=/dev/shm
'_EOF_'
    # << happy emacs

    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
        -chainMinScore=3000 -chainLinearGap=medium \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > do.log 2>&1
    # real    1423m17.538s

    cat fb.hg38.chainConCri1Link.txt
    # 1095032620 bases of 3049335806 (35.911%) in intersection
    # replacing the previous tuned version:
    # 1007403174 bases of 3049335806 (33.037%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` hg38 conCri1) > rbest.log 2>&1 &
    # real    99m34.655s

    # and for the swap:
    mkdir /hive/data/genomes/conCri1/bed/blastz.hg38.swap
    cd /hive/data/genomes/conCri1/bed/blastz.hg38.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/hg38/bed/lastzConCri1.2015-04-28/DEF \
        -swap -chainMinScore=3000 -chainLinearGap=medium \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    #  real    81m47.687s

    cat fb.conCri1.chainHg38Link.txt
    # 1026633109 bases of 1682542007 (61.017%) in intersection
    # replacing the previous tuned version:
    # 946409492 bases of 1682542007 (56.249%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` conCri1 hg38) > rbest.log 2>&1
    # real    415m57.506s finished manually real    45m44.330s
    time (doRecipBest.pl -workhorse=hgwdev -continue=download \
       -buildDir=`pwd` conCri1 hg38) > rbestDownload.log 2>&1
    # real    0m4.444s

#########################################################################
# LASTZ human/hg38 vs. brush tailed rat/octDeg1 - (DONE - 2015-04-24 - Hiram)
    mkdir /hive/data/genomes/hg38/bed/lastzOctDeg1.2015-04-24
    cd /hive/data/genomes/hg38/bed/lastzOctDeg1.2015-04-24

# parameters obtained from a tuning run of lastz_D
# /hive/users/hiram/multiz/100way/hg38.octDeg1/hg38.octDeg.tuning.top400.txt
    cp -p /hive/users/hiram/multiz/100way/hg38.octDeg1/hg38.octDeg1.tuning.top400.txt ./hg38.octDeg1.tuning.Q.txt

    cat << '_EOF_' > DEF
# human vs brush tailed rat
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz
BLASTZ_O=400
BLASTZ_E=30
BLASTZ_M=254
# default BLASTZ_Q score matrix:
#       A     C     G     T
# A    91  -114   -31  -123
# C  -114   100  -125   -31
# G   -31  -125   100  -114
# T  -123   -31  -114    91

# TARGET: human hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CTGDIR=/hive/data/genomes/hg38/hg38.contigs.2bit
SEQ1_CTGLEN=/hive/data/genomes/hg38/hg38.contigs.chrom.sizes
SEQ1_LIFT=/hive/data/genomes/hg38/jkStuff/hg38.contigs.lift
SEQ1_CHUNK=40000000
SEQ1_LIMIT=30
SEQ1_LAP=10000

# QUERY: brush tailed rat octDeg1
SEQ2_DIR=/hive/data/genomes/octDeg1/octDeg1.2bit
SEQ2_LEN=/hive/data/genomes/octDeg1/chrom.sizes
SEQ2_CHUNK=20000000
SEQ2_LIMIT=30
SEQ2_LAP=0

BASE=/hive/data/genomes/hg38/bed/lastzOctDeg1.2015-04-24
TMPDIR=/dev/shm
'_EOF_'
    # << happy emacs

    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
        -chainMinScore=3000 -chainLinearGap=medium \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > do.log 2>&1
    # real    311m38.376s

    cat fb.hg38.chainOctDeg1Link.txt
    # 1226996880 bases of 3049335806 (40.238%) in intersection
    # replacing the previous tuned version:
    # 1092487806 bases of 3049335806 (35.827%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` hg38 octDeg1) > rbest.log 2>&1 &
    # real    36m11.781s

    # and for the swap:
    mkdir /hive/data/genomes/octDeg1/bed/blastz.hg38.swap
    cd /hive/data/genomes/octDeg1/bed/blastz.hg38.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/hg38/bed/lastzOctDeg1.2015-04-24/DEF \
        -swap -chainMinScore=3000 -chainLinearGap=medium \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    #  real    107m48.695s

    cat fb.octDeg1.chainHg38Link.txt
    # 1203795092 bases of 2526254702 (47.651%) in intersection
    # replacing the previous tuned version:
    # 1076649085 bases of 2526254702 (42.618%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` octDeg1 hg38) > rbest.log 2>&1
    # real    38m52.487s

#########################################################################
# LASTZ human/hg38 vs. pika/ochPri3 - (DONE - 2015-04-17 - Hiram)
    # mistakenly done in directory name 2015-04-17 when it is really 2015-04-27
    mkdir /hive/data/genomes/hg38/bed/lastzOchPri3.2015-04-17
    cd /hive/data/genomes/hg38/bed/lastzOchPri3.2015-04-17

    cat << '_EOF_' > DEF
# human vs pika
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz
BLASTZ_O=400
BLASTZ_E=30
BLASTZ_M=254
# default BLASTZ_Q score matrix:
#       A     C     G     T
# A    91  -114   -31  -123
# C  -114   100  -125   -31
# G   -31  -125   100  -114
# T  -123   -31  -114    91

# TARGET: human hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CTGDIR=/hive/data/genomes/hg38/hg38.contigs.2bit
SEQ1_CTGLEN=/hive/data/genomes/hg38/hg38.contigs.chrom.sizes
SEQ1_LIFT=/hive/data/genomes/hg38/jkStuff/hg38.contigs.lift
SEQ1_CHUNK=40000000
SEQ1_LIMIT=30
SEQ1_LAP=10000

# QUERY: pika ochPri3
SEQ2_DIR=/hive/data/genomes/ochPri3/ochPri3.2bit
SEQ2_LEN=/hive/data/genomes/ochPri3/chrom.sizes
SEQ2_CHUNK=20000000
SEQ2_LIMIT=30
SEQ2_LAP=0

BASE=/hive/data/genomes/hg38/bed/lastzOchPri3.2015-04-17
TMPDIR=/dev/shm
'_EOF_'
    # << happy emacs

    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
        -chainMinScore=3000 -chainLinearGap=medium \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > do.log 2>&1
    # real    971m36.115s

    cat fb.hg38.chainOchPri3Link.txt
    # 1025119076 bases of 3049335806 (33.618%) in intersection
    # replacing the previous tuned version:
    # 922764468 bases of 3049335806 (30.261%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` hg38 ochPri3) > rbest.log 2>&1 &
    # real    35m7.253s

    # and for the swap:
    mkdir /hive/data/genomes/ochPri3/bed/blastz.hg38.swap
    cd /hive/data/genomes/ochPri3/bed/blastz.hg38.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/hg38/bed/lastzOchPri3.2015-04-17/DEF \
        -swap -chainMinScore=3000 -chainLinearGap=medium \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    #  real    80m33.697s

    cat fb.ochPri3.chainHg38Link.txt
    # 968829838 bases of 1943987870 (49.837%) in intersection
    # replacing the previous tuned version:
    # 874404292 bases of 1943987870 (44.980%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` ochPri3 hg38) > rbest.log 2>&1
    # real    46m26.106s

#########################################################################
# LASTZ human/hg38 vs. hedgehog/eriEur2 - (DONE - 2015-02-17 - Hiram)
    mkdir /hive/data/genomes/hg38/bed/lastzEriEur2.2015-02-17
    cd /hive/data/genomes/hg38/bed/lastzEriEur2.2015-02-17

    cat << '_EOF_' > DEF
# human vs hedgehog
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.54/bin/lastz
BLASTZ_O=400
BLASTZ_E=30

# TARGET: human hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CTGDIR=/hive/data/genomes/hg38/hg38.contigs.2bit
SEQ1_CTGLEN=/hive/data/genomes/hg38/hg38.contigs.chrom.sizes
SEQ1_LIFT=/hive/data/genomes/hg38/jkStuff/hg38.contigs.lift
SEQ1_CHUNK=40000000
SEQ1_LIMIT=30
SEQ1_LAP=10000

# QUERY: hedgehog eriEur2
SEQ2_DIR=/hive/data/genomes/eriEur2/eriEur2.2bit
SEQ2_LEN=/hive/data/genomes/eriEur2/chrom.sizes
SEQ2_CHUNK=20000000
SEQ2_LIMIT=30
SEQ2_LAP=0

BASE=/hive/data/genomes/hg38/bed/lastzEriEur2.2015-02-17
TMPDIR=/dev/shm
'_EOF_'
    # << happy emacs

    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
        -chainMinScore=3000 -chainLinearGap=medium \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > do.log 2>&1
    #  real    2763m20.266s

    cat fb.hg38.chainEriEur2Link.txt
    # 777213928 bases of 3049335806 (25.488%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` hg38 eriEur2) \
       > rbest.log 2>&1 &
    # real    32m54.605s

    # and for the swap:
    mkdir /hive/data/genomes/eriEur2/bed/blastz.hg38.swap
    cd /hive/data/genomes/eriEur2/bed/blastz.hg38.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/hg38/bed/lastzEriEur2.2015-02-17/DEF \
        -swap -chainMinScore=3000 -chainLinearGap=medium \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    #  real    75m12.828s

    cat fb.eriEur2.chainHg38Link.txt
    # 730172579 bases of 2333073535 (31.297%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` eriEur2 hg38) \
       > rbest.log 2>&1
    # real    34m37.153s

#########################################################################
# LASTZ human/hg38 vs. tenrec/echTel2 - (DONE - 2015-04-28 - Hiram)
    mkdir /hive/data/genomes/hg38/bed/lastzEchTel2.2015-04-28
    cd /hive/data/genomes/hg38/bed/lastzEchTel2.2015-04-28

    cat << '_EOF_' > DEF
# human vs tenrec
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz
BLASTZ_O=400
BLASTZ_E=30
BLASTZ_M=254
# default BLASTZ_Q score matrix:
#       A     C     G     T
# A    91  -114   -31  -123
# C  -114   100  -125   -31
# G   -31  -125   100  -114
# T  -123   -31  -114    91

# TARGET: human hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CTGDIR=/hive/data/genomes/hg38/hg38.contigs.2bit
SEQ1_CTGLEN=/hive/data/genomes/hg38/hg38.contigs.chrom.sizes
SEQ1_LIFT=/hive/data/genomes/hg38/jkStuff/hg38.contigs.lift
SEQ1_CHUNK=40000000
SEQ1_LIMIT=30
SEQ1_LAP=10000

# QUERY: tenrec echTel2
SEQ2_DIR=/hive/data/genomes/echTel2/echTel2.2bit
SEQ2_LEN=/hive/data/genomes/echTel2/chrom.sizes
SEQ2_CHUNK=20000000
SEQ2_LIMIT=30
SEQ2_LAP=0

BASE=/hive/data/genomes/hg38/bed/lastzEchTel2.2015-04-28
TMPDIR=/dev/shm
'_EOF_'
    # << happy emacs

    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
        -chainMinScore=3000 -chainLinearGap=medium \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > do.log 2>&1
    # real    1689m14.948s

    cat fb.hg38.chainEchTel2Link.txt
    # 893752189 bases of 3049335806 (29.310%) in intersection
    # replacing the previous tuned version:
    # 840080104 bases of 3049335806 (27.550%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` hg38 echTel2) > rbest.log 2>&1 &
    # real    108m5.914s

    # and for the swap:
    mkdir /hive/data/genomes/echTel2/bed/blastz.hg38.swap
    cd /hive/data/genomes/echTel2/bed/blastz.hg38.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/hg38/bed/lastzEchTel2.2015-04-28/DEF \
        -swap -chainMinScore=3000 -chainLinearGap=medium \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    #  real    87m14.342s

    cat fb.echTel2.chainHg38Link.txt
    # 853272550 bases of 2605196361 (32.753%) in intersection
    # replacing the previous tuned version:
    # 802302160 bases of 2605196361 (30.796%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` echTel2 hg38) \
      > rbest.log 2>&1
    # real    42m32.249s

#########################################################################
# LASTZ human/hg38 vs. rat/rn6 - (DONE - 2015-02-14 - Hiram)
    mkdir /hive/data/genomes/hg38/bed/lastzRn6.2015-02-14
    cd /hive/data/genomes/hg38/bed/lastzRn6.2015-02-14

# parameters obtained from a tuning run of lastz_D
# /hive/users/hiram/multiz/100way/hg38.rn6/hg38.octDeg.tuning.top400.txt
    cp -p /hive/users/hiram/multiz/100way/hg38.rn6/hg38.rn6.tuning.top400.txt ./hg38.rn6.tuning.Q.txt

    cat << '_EOF_' > DEF
# human vs rat
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.54/bin/lastz
BLASTZ_O=400
BLASTZ_E=30

# TARGET: human hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CTGDIR=/hive/data/genomes/hg38/hg38.contigs.2bit
SEQ1_CTGLEN=/hive/data/genomes/hg38/hg38.contigs.chrom.sizes
SEQ1_LIFT=/hive/data/genomes/hg38/jkStuff/hg38.contigs.lift
SEQ1_CHUNK=40000000
SEQ1_LIMIT=30
SEQ1_LAP=10000

# QUERY: rat rn6
SEQ2_DIR=/hive/data/genomes/rn6/rn6.2bit
SEQ2_LEN=/hive/data/genomes/rn6/chrom.sizes
SEQ2_CHUNK=20000000
SEQ2_LIMIT=30
SEQ2_LAP=0

BASE=/hive/data/genomes/hg38/bed/lastzRn6.2015-02-14
TMPDIR=/dev/shm
'_EOF_'
    # << happy emacs

    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
        -chainMinScore=3000 -chainLinearGap=medium \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > do.log 2>&1
    # real    539m6.068s

    cat fb.hg38.chainRn6Link.txt
    # 947631744 bases of 3049335806 (31.077%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` hg38 rn6) > rbest.log 2>&1 &
    # real    61m44.574s

    # and for the swap:
    mkdir /hive/data/genomes/rn6/bed/blastz.hg38.swap
    cd /hive/data/genomes/rn6/bed/blastz.hg38.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/hg38/bed/lastzRn6.2015-02-14/DEF \
        -swap -chainMinScore=3000 -chainLinearGap=medium \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    #  real    114m13.019s

    cat fb.rn6.chainHg38Link.txt
    # 952700446 bases of 2729860805 (34.899%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` rn6 hg38) > rbest.log 2>&1
    # real    47m8.081s

#########################################################################
# LASTZ human/hg38 vs. Chinese hamster/criGri1 - (DONE - 2015-02-17 - Hiram)
    mkdir /hive/data/genomes/hg38/bed/lastzCriGri1.2015-02-17
    cd /hive/data/genomes/hg38/bed/lastzCriGri1.2015-02-17

    cat << '_EOF_' > DEF
# human vs Chinese hamster
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.54/bin/lastz
BLASTZ_O=400
BLASTZ_E=30

# TARGET: human hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CTGDIR=/hive/data/genomes/hg38/hg38.contigs.2bit
SEQ1_CTGLEN=/hive/data/genomes/hg38/hg38.contigs.chrom.sizes
SEQ1_LIFT=/hive/data/genomes/hg38/jkStuff/hg38.contigs.lift
SEQ1_CHUNK=40000000
SEQ1_LIMIT=30
SEQ1_LAP=10000

# QUERY: Chinese hamster criGri1
SEQ2_DIR=/hive/data/genomes/criGri1/criGri1.2bit
SEQ2_LEN=/hive/data/genomes/criGri1/chrom.sizes
SEQ2_CHUNK=20000000
SEQ2_LIMIT=100
SEQ2_LAP=0

BASE=/hive/data/genomes/hg38/bed/lastzCriGri1.2015-02-17
TMPDIR=/dev/shm
'_EOF_'
    # << happy emacs

    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
        -chainMinScore=3000 -chainLinearGap=medium \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > do.log 2>&1
    # real    3327m39.074s
    # after a crash in lastz, continuing:
    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
        -chainMinScore=3000 -chainLinearGap=medium \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -continue=cat -syntenicNet) > cat.log 2>&1
    # real    399m26.683s

    cat fb.hg38.chainCriGri1Link.txt
    # 1011432843 bases of 3049335806 (33.169%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` hg38 criGri1) \
       > rbest.log 2>&1 &
    # lost the log file
    # real    41m11.272s

    # and for the swap:
    mkdir /hive/data/genomes/criGri1/bed/blastz.hg38.swap
    cd /hive/data/genomes/criGri1/bed/blastz.hg38.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/hg38/bed/lastzCriGri1.2015-02-17/DEF \
        -swap -chainMinScore=3000 -chainLinearGap=medium \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    #  real    142m31.834s

    cat fb.criGri1.chainHg38Link.txt
    # 976365873 bases of 2301325917 (42.426%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` criGri1 hg38) \
       > rbest.log 2>&1
    # real    44m9.075s

#########################################################################
# LASTZ human/hg38 vs. Golden hamster/mesAur1 - (DONE - 2015-02-17 - Hiram)
    mkdir /hive/data/genomes/hg38/bed/lastzMesAur1.2015-02-17
    cd /hive/data/genomes/hg38/bed/lastzMesAur1.2015-02-17

    cat << '_EOF_' > DEF
# human vs Golden hamster
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.54/bin/lastz
BLASTZ_O=400
BLASTZ_E=30

# TARGET: human hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CTGDIR=/hive/data/genomes/hg38/hg38.contigs.2bit
SEQ1_CTGLEN=/hive/data/genomes/hg38/hg38.contigs.chrom.sizes
SEQ1_LIFT=/hive/data/genomes/hg38/jkStuff/hg38.contigs.lift
SEQ1_CHUNK=40000000
SEQ1_LIMIT=30
SEQ1_LAP=10000

# QUERY: Golden hamster mesAur1
SEQ2_DIR=/hive/data/genomes/mesAur1/mesAur1.2bit
SEQ2_LEN=/hive/data/genomes/mesAur1/chrom.sizes
SEQ2_CHUNK=20000000
SEQ2_LIMIT=50
SEQ2_LAP=0

BASE=/hive/data/genomes/hg38/bed/lastzMesAur1.2015-02-17
TMPDIR=/dev/shm
'_EOF_'
    # << happy emacs

    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
        -chainMinScore=3000 -chainLinearGap=medium \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > do.log 2>&1
    # real    3321m29.849s

    cat fb.hg38.chainMesAur1Link.txt
    # 939276772 bases of 3049335806 (30.803%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` hg38 mesAur1) \
       > rbest.log 2>&1 &
    # real    40m43.963s

    # and for the swap:
    mkdir /hive/data/genomes/mesAur1/bed/blastz.hg38.swap
    cd /hive/data/genomes/mesAur1/bed/blastz.hg38.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/hg38/bed/lastzMesAur1.2015-02-17/DEF \
        -swap -chainMinScore=3000 -chainLinearGap=medium \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    #  real    97m31.454s

    cat fb.mesAur1.chainHg38Link.txt
    # 894722574 bases of 2076176254 (43.095%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` mesAur1 hg38) \
       > rbest.log 2>&1
    # real    43m18.764s

#########################################################################
# LASTZ human/hg38 vs. Prairie vole/micOch1 - (DONE - 2015-02-14 - Hiram)
    mkdir /hive/data/genomes/hg38/bed/lastzMicOch1.2015-02-14
    cd /hive/data/genomes/hg38/bed/lastzMicOch1.2015-02-14

    cat << '_EOF_' > DEF
# human vs Prairie vole
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.54/bin/lastz

# TARGET: human hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CTGDIR=/hive/data/genomes/hg38/hg38.contigs.2bit
SEQ1_CTGLEN=/hive/data/genomes/hg38/hg38.contigs.chrom.sizes
SEQ1_LIFT=/hive/data/genomes/hg38/jkStuff/hg38.contigs.lift
SEQ1_CHUNK=40000000
SEQ1_LIMIT=30
SEQ1_LAP=10000

# QUERY: Prairie vole micOch1
SEQ2_DIR=/hive/data/genomes/micOch1/micOch1.2bit
SEQ2_LEN=/hive/data/genomes/micOch1/chrom.sizes
SEQ2_CHUNK=20000000
SEQ2_LIMIT=20
SEQ2_LAP=0

BASE=/hive/data/genomes/hg38/bed/lastzMicOch1.2015-02-14
TMPDIR=/dev/shm
'_EOF_'
    # << happy emacs

    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
        -chainMinScore=3000 -chainLinearGap=medium \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > do.log 2>&1
    # real    493m1.575s

    cat fb.hg38.chainMicOch1Link.txt
    # 960200428 bases of 3049335806 (31.489%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` hg38 micOch1) > rbest.log 2>&1 &
    # real    28m17.738s

    # and for the swap:
    mkdir /hive/data/genomes/micOch1/bed/blastz.hg38.swap
    cd /hive/data/genomes/micOch1/bed/blastz.hg38.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/hg38/bed/lastzMicOch1.2015-02-14/DEF \
        -swap -chainMinScore=3000 -chainLinearGap=medium \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    #  real    111m26.473s

    cat fb.micOch1.chainHg38Link.txt
    # 916196683 bases of 2104321675 (43.539%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` micOch1 hg38) > rbest.log 2>&1
    # real    84m4.019s

#########################################################################
# LASTZ human/hg38 vs. shrew/sorAra2 - (DONE - 2015-02-17 - Hiram)
    mkdir /hive/data/genomes/hg38/bed/lastzSorAra2.2015-02-17
    cd /hive/data/genomes/hg38/bed/lastzSorAra2.2015-02-17

    cat << '_EOF_' > DEF
# human vs shrew
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.54/bin/lastz
BLASTZ_O=400
BLASTZ_E=30

# TARGET: human hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CTGDIR=/hive/data/genomes/hg38/hg38.contigs.2bit
SEQ1_CTGLEN=/hive/data/genomes/hg38/hg38.contigs.chrom.sizes
SEQ1_LIFT=/hive/data/genomes/hg38/jkStuff/hg38.contigs.lift
SEQ1_CHUNK=40000000
SEQ1_LIMIT=30
SEQ1_LAP=10000

# QUERY: shrew sorAra2
SEQ2_DIR=/hive/data/genomes/sorAra2/sorAra2.2bit
SEQ2_LEN=/hive/data/genomes/sorAra2/chrom.sizes
SEQ2_CHUNK=20000000
SEQ2_LIMIT=20
SEQ2_LAP=0

BASE=/hive/data/genomes/hg38/bed/lastzSorAra2.2015-02-17
TMPDIR=/dev/shm
'_EOF_'
    # << happy emacs

    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
        -chainMinScore=3000 -chainLinearGap=medium \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > do.log 2>&1
    # real    3480m4.393s

    cat fb.hg38.chainSorAra2Link.txt
    # 820409269 bases of 3049335806 (26.905%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` hg38 sorAra2) \
       > rbest.log 2>&1 &
    # real    37m5.305s

    # and for the swap:
    mkdir /hive/data/genomes/sorAra2/bed/blastz.hg38.swap
    cd /hive/data/genomes/sorAra2/bed/blastz.hg38.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/hg38/bed/lastzSorAra2.2015-02-17/DEF \
        -swap -chainMinScore=3000 -chainLinearGap=medium \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    #  real    106m55.651s

    cat fb.sorAra2.chainHg38Link.txt
    # 783891768 bases of 2192103426 (35.760%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` sorAra2 hg38) \
       > rbest.log 2>&1
    # real    37m44.557s

#########################################################################
# LASTZ human/hg38 vs. wallaby/macEug2 - (DONE - 2015-02-17 - Hiram)
    mkdir /hive/data/genomes/hg38/bed/lastzMacEug2.2015-02-17
    cd /hive/data/genomes/hg38/bed/lastzMacEug2.2015-02-17

    cat << '_EOF_' > DEF
# human vs wallaby
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.54/bin/lastz
BLASTZ_O=400
BLASTZ_E=30

# TARGET: human hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CTGDIR=/hive/data/genomes/hg38/hg38.contigs.2bit
SEQ1_CTGLEN=/hive/data/genomes/hg38/hg38.contigs.chrom.sizes
SEQ1_LIFT=/hive/data/genomes/hg38/jkStuff/hg38.contigs.lift
SEQ1_CHUNK=40000000
SEQ1_LIMIT=30
SEQ1_LAP=10000

# QUERY: wallaby macEug2
SEQ2_DIR=/hive/data/genomes/macEug2/macEug2.2bit
SEQ2_LEN=/hive/data/genomes/macEug2/chrom.sizes
SEQ2_CHUNK=20000000
SEQ2_LIMIT=300
SEQ2_LAP=0

BASE=/hive/data/genomes/hg38/bed/lastzMacEug2.2015-02-17
TMPDIR=/dev/shm
'_EOF_'
    # << happy emacs

    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
        -chainMinScore=5000 -chainLinearGap=loose \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > do.log 2>&1
    # real    3321m43.912s

    cat fb.hg38.chainMacEug2Link.txt
    # 194475426 bases of 3049335806 (6.378%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` hg38 macEug2) \
       > rbest.log 2>&1 &
    # real    17m42.993s

    # and for the swap:
    mkdir /hive/data/genomes/macEug2/bed/blastz.hg38.swap
    cd /hive/data/genomes/macEug2/bed/blastz.hg38.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/hg38/bed/lastzMacEug2.2015-02-17/DEF \
        -swap -chainMinScore=5000 -chainLinearGap=loose \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    #  real    185m57.086s

    cat fb.macEug2.chainHg38Link.txt
    # 182916846 bases of 2536076957 (7.213%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` macEug2 hg38) \
       > rbest.log 2>&1
    # real    143m14.162s

#########################################################################
# LASTZ human/hg38 vs. Tasmanian devil/sarHar1 - (DONE - 2015-02-13 - Hiram)
    mkdir /hive/data/genomes/hg38/bed/lastzSarHar1.2015-02-13
    cd /hive/data/genomes/hg38/bed/lastzSarHar1.2015-02-13

    cat << '_EOF_' > DEF
# human vs Tasmanian devil
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.54/bin/lastz
BLASTZ_O=400
BLASTZ_E=30
BLASTZ_Y=3400
BLASTZ_L=6000
BLASTZ_K=2200
BLASTZ_M=50
BLASTZ_Q=/scratch/data/blastz/HoxD55.q
#      A    C    G    T
#     91  -90  -25 -100
#    -90  100 -100  -25
#    -25 -100  100  -90
#   -100  -25  -90  91

# TARGET: human hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CTGDIR=/hive/data/genomes/hg38/hg38.contigs.2bit
SEQ1_CTGLEN=/hive/data/genomes/hg38/hg38.contigs.chrom.sizes
SEQ1_LIFT=/hive/data/genomes/hg38/jkStuff/hg38.contigs.lift
SEQ1_CHUNK=40000000
SEQ1_LIMIT=30
SEQ1_LAP=10000

# QUERY: Tasmanian devil sarHar1
SEQ2_DIR=/hive/data/genomes/sarHar1/sarHar1.2bit
SEQ2_LEN=/hive/data/genomes/sarHar1/chrom.sizes
SEQ2_CHUNK=20000000
SEQ2_LIMIT=60
SEQ2_LAP=0

BASE=/hive/data/genomes/hg38/bed/lastzSarHar1.2015-02-13
TMPDIR=/dev/shm
'_EOF_'
    # << happy emacs

    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
        -chainMinScore=5000 -chainLinearGap=loose \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > do.log 2>&1
    # real    862m32.202s

    cat fb.hg38.chainSarHar1Link.txt
    # 388903768 bases of 3049335806 (12.754%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` hg38 sarHar1) > rbest.log 2>&1 &
    # real    34m31.714s

    # and for the swap:
    mkdir /hive/data/genomes/sarHar1/bed/blastz.hg38.swap
    cd /hive/data/genomes/sarHar1/bed/blastz.hg38.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/hg38/bed/lastzSarHar1.2015-02-13/DEF \
        -swap -chainMinScore=5000 -chainLinearGap=loose \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    # real    69m33.260s

    cat fb.sarHar1.chainHg38Link.txt
    # 378889609 bases of 2931539702 (12.925%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` sarHar1 hg38) > rbest.log 2>&1
    # real    22m1.912s

#########################################################################
# LASTZ human/hg38 vs. Spiny softshell turtle/apaSpi1 - (DONE - 2015-02-13 - Hiram)
    mkdir /hive/data/genomes/hg38/bed/lastzApaSpi1.2015-02-13
    cd /hive/data/genomes/hg38/bed/lastzApaSpi1.2015-02-13

    cat << '_EOF_' > DEF
# human vs Spiny softshell turtle
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.54/bin/lastz
BLASTZ_O=400
BLASTZ_E=30
BLASTZ_Y=3400
BLASTZ_L=6000
BLASTZ_K=2200
BLASTZ_M=50
BLASTZ_Q=/scratch/data/blastz/HoxD55.q
#      A    C    G    T
#     91  -90  -25 -100
#    -90  100 -100  -25
#    -25 -100  100  -90
#   -100  -25  -90  91

# TARGET: human hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CTGDIR=/hive/data/genomes/hg38/hg38.contigs.2bit
SEQ1_CTGLEN=/hive/data/genomes/hg38/hg38.contigs.chrom.sizes
SEQ1_LIFT=/hive/data/genomes/hg38/jkStuff/hg38.contigs.lift
SEQ1_CHUNK=40000000
SEQ1_LIMIT=30
SEQ1_LAP=10000

# QUERY: Spiny softshell turtle apaSpi1
SEQ2_DIR=/hive/data/genomes/apaSpi1/apaSpi1.2bit
SEQ2_LEN=/hive/data/genomes/apaSpi1/chrom.sizes
SEQ2_CHUNK=20000000
SEQ2_LIMIT=400
SEQ2_LAP=0

BASE=/hive/data/genomes/hg38/bed/lastzApaSpi1.2015-02-13
TMPDIR=/dev/shm
'_EOF_'
    # << happy emacs

    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
        -chainMinScore=5000 -chainLinearGap=loose \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > do.log 2>&1
    # real    737m19.211s

    cat fb.hg38.chainApaSpi1Link.txt
    # 140617559 bases of 3049335806 (4.611%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` hg38 apaSpi1) > rbest.log 2>&1 &
    # real    19m56.198s

    # and for the swap:
    mkdir /hive/data/genomes/apaSpi1/bed/blastz.hg38.swap
    cd /hive/data/genomes/apaSpi1/bed/blastz.hg38.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/hg38/bed/lastzApaSpi1.2015-02-13/DEF \
        -swap -chainMinScore=5000 -chainLinearGap=loose \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    #  real    47m41.422s

    cat fb.apaSpi1.chainHg38Link.txt
    # 118690974 bases of 1877982184 (6.320%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` apaSpi1 hg38) > rbest.log 2>&1
    # real    48m11.487s

#########################################################################
# LASTZ human/hg38 vs. Chinese softshell turtle/pelSin1 - (DONE - 2015-02-13 - Hiram)
    mkdir /hive/data/genomes/hg38/bed/lastzPelSin1.2015-02-13
    cd /hive/data/genomes/hg38/bed/lastzPelSin1.2015-02-13

    cat << '_EOF_' > DEF
# human vs Chinese softshell turtle
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.54/bin/lastz
BLASTZ_O=400
BLASTZ_E=30
BLASTZ_Y=3400
BLASTZ_L=6000
BLASTZ_K=2200
BLASTZ_M=50
BLASTZ_Q=/scratch/data/blastz/HoxD55.q
#      A    C    G    T
#     91  -90  -25 -100
#    -90  100 -100  -25
#    -25 -100  100  -90
#   -100  -25  -90  91

# TARGET: human hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CTGDIR=/hive/data/genomes/hg38/hg38.contigs.2bit
SEQ1_CTGLEN=/hive/data/genomes/hg38/hg38.contigs.chrom.sizes
SEQ1_LIFT=/hive/data/genomes/hg38/jkStuff/hg38.contigs.lift
SEQ1_CHUNK=40000000
SEQ1_LIMIT=30
SEQ1_LAP=10000

# QUERY: Chinese softshell turtle pelSin1
SEQ2_DIR=/hive/data/genomes/pelSin1/pelSin1.2bit
SEQ2_LEN=/hive/data/genomes/pelSin1/chrom.sizes
SEQ2_CHUNK=20000000
SEQ2_LIMIT=30
SEQ2_LAP=0

BASE=/hive/data/genomes/hg38/bed/lastzPelSin1.2015-02-13
TMPDIR=/dev/shm
'_EOF_'
    # << happy emacs

    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
        -chainMinScore=5000 -chainLinearGap=loose \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > do.log 2>&1
    # real    749m6.906s

    cat fb.hg38.chainPelSin1Link.txt
    # 174304542 bases of 3049335806 (5.716%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` hg38 pelSin1) > rbest.log 2>&1 &
    # real    32m56.986s

    # and for the swap:
    mkdir /hive/data/genomes/pelSin1/bed/blastz.hg38.swap
    cd /hive/data/genomes/pelSin1/bed/blastz.hg38.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/hg38/bed/lastzPelSin1.2015-02-13/DEF \
        -swap -chainMinScore=5000 -chainLinearGap=loose \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    # real    28m15.790s

    cat fb.pelSin1.chainHg38Link.txt
    # 151827556 bases of 2106639384 (7.207%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` pelSin1 hg38) > rbest.log 2>&1
    # real    63m22.391s

#########################################################################
# LASTZ human/hg38 vs. platypus/ornAna1 - (DONE - 2015-02-13 - Hiram)
    mkdir /hive/data/genomes/hg38/bed/lastzOrnAna1.2015-02-13
    cd /hive/data/genomes/hg38/bed/lastzOrnAna1.2015-02-13

    cat << '_EOF_' > DEF
# human vs platypus
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.54/bin/lastz
BLASTZ_O=400
BLASTZ_E=30
BLASTZ_Y=3400
BLASTZ_L=6000
BLASTZ_K=2200
BLASTZ_M=50
BLASTZ_Q=/scratch/data/blastz/HoxD55.q
#      A    C    G    T
#     91  -90  -25 -100
#    -90  100 -100  -25
#    -25 -100  100  -90
#   -100  -25  -90  91

# TARGET: human hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CTGDIR=/hive/data/genomes/hg38/hg38.contigs.2bit
SEQ1_CTGLEN=/hive/data/genomes/hg38/hg38.contigs.chrom.sizes
SEQ1_LIFT=/hive/data/genomes/hg38/jkStuff/hg38.contigs.lift
SEQ1_CHUNK=40000000
SEQ1_LIMIT=30
SEQ1_LAP=10000

# QUERY: platypus ornAna1
SEQ2_DIR=/hive/data/genomes/ornAna1/ornAna1.2bit
SEQ2_LEN=/hive/data/genomes/ornAna1/chrom.sizes
SEQ2_CHUNK=20000000
SEQ2_LIMIT=300
SEQ2_LAP=0

BASE=/hive/data/genomes/hg38/bed/lastzOrnAna1.2015-02-13
TMPDIR=/dev/shm
'_EOF_'
    # << happy emacs

    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
        -chainMinScore=5000 -chainLinearGap=loose \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > do.log 2>&1
    # real    714m38.972s

    cat fb.hg38.chainOrnAna1Link.txt
    # 236893911 bases of 3049335806 (7.769%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` hg38 ornAna1) > rbest.log 2>&1 &
    # real    38m4.653s

    # and for the swap:
    mkdir /hive/data/genomes/ornAna1/bed/blastz.hg38.swap
    cd /hive/data/genomes/ornAna1/bed/blastz.hg38.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/hg38/bed/lastzOrnAna1.2015-02-13/DEF \
        -swap -chainMinScore=5000 -chainLinearGap=loose \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    #  real    84m45.882s

    cat fb.ornAna1.chainHg38Link.txt
    # 217095490 bases of 1842236818 (11.784%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` ornAna1 hg38) > rbest.log 2>&1
    # real    61m34.921s

#########################################################################
# LASTZ human/hg38 vs. American alligator/allMis1 - (DONE - 2015-02-13 - Hiram)
    mkdir /hive/data/genomes/hg38/bed/lastzAllMis1.2015-02-13
    cd /hive/data/genomes/hg38/bed/lastzAllMis1.2015-02-13

    cat << '_EOF_' > DEF
# human vs American alligator
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.54/bin/lastz
BLASTZ_O=400
BLASTZ_E=30
BLASTZ_Y=3400
BLASTZ_L=6000
BLASTZ_K=2200
BLASTZ_M=50
BLASTZ_Q=/scratch/data/blastz/HoxD55.q
#      A    C    G    T
#     91  -90  -25 -100
#    -90  100 -100  -25
#    -25 -100  100  -90
#   -100  -25  -90  91

# TARGET: human hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CTGDIR=/hive/data/genomes/hg38/hg38.contigs.2bit
SEQ1_CTGLEN=/hive/data/genomes/hg38/hg38.contigs.chrom.sizes
SEQ1_LIFT=/hive/data/genomes/hg38/jkStuff/hg38.contigs.lift
SEQ1_CHUNK=40000000
SEQ1_LIMIT=30
SEQ1_LAP=10000

# QUERY: American alligator allMis1
SEQ2_DIR=/hive/data/genomes/allMis1/allMis1.2bit
SEQ2_LEN=/hive/data/genomes/allMis1/chrom.sizes
SEQ2_CHUNK=20000000
SEQ2_LIMIT=30
SEQ2_LAP=0

BASE=/hive/data/genomes/hg38/bed/lastzAllMis1.2015-02-13
TMPDIR=/dev/shm
'_EOF_'
    # << happy emacs

    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
        -chainMinScore=5000 -chainLinearGap=loose \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > do.log 2>&1
    # real    773m58.250s

    cat fb.hg38.chainAllMis1Link.txt
    # 230567044 bases of 3049335806 (7.561%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` hg38 allMis1) > rbest.log 2>&1 &
    # real    32m25.167s

    # and for the swap:
    mkdir /hive/data/genomes/allMis1/bed/blastz.hg38.swap
    cd /hive/data/genomes/allMis1/bed/blastz.hg38.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/hg38/bed/lastzAllMis1.2015-02-13/DEF \
        -swap -chainMinScore=5000 -chainLinearGap=loose \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    #  real    41m40.053s

    cat fb.allMis1.chainHg38Link.txt
    # 184529544 bases of 2129659933 (8.665%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` allMis1 hg38) > rbest.log 2>&1
    # real    20m37.259s

#########################################################################
# LASTZ human/hg38 vs. Rock pigeon/colLiv1 - (DONE - 2015-02-13 - Hiram)
    mkdir /hive/data/genomes/hg38/bed/lastzColLiv1.2015-02-13
    cd /hive/data/genomes/hg38/bed/lastzColLiv1.2015-02-13

    cat << '_EOF_' > DEF
# human vs Rock pigeon
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.54/bin/lastz
BLASTZ_O=400
BLASTZ_E=30
BLASTZ_Y=3400
BLASTZ_L=6000
BLASTZ_K=2200
BLASTZ_M=50
BLASTZ_Q=/scratch/data/blastz/HoxD55.q
#      A    C    G    T
#     91  -90  -25 -100
#    -90  100 -100  -25
#    -25 -100  100  -90
#   -100  -25  -90  91

# TARGET: human hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CTGDIR=/hive/data/genomes/hg38/hg38.contigs.2bit
SEQ1_CTGLEN=/hive/data/genomes/hg38/hg38.contigs.chrom.sizes
SEQ1_LIFT=/hive/data/genomes/hg38/jkStuff/hg38.contigs.lift
SEQ1_CHUNK=40000000
SEQ1_LIMIT=30
SEQ1_LAP=10000

# QUERY: Rock pigeon colLiv1
SEQ2_DIR=/hive/data/genomes/colLiv1/colLiv1.2bit
SEQ2_LEN=/hive/data/genomes/colLiv1/chrom.sizes
SEQ2_CHUNK=20000000
SEQ2_LIMIT=30
SEQ2_LAP=0

BASE=/hive/data/genomes/hg38/bed/lastzColLiv1.2015-02-13
TMPDIR=/dev/shm
'_EOF_'
    # << happy emacs

    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
        -chainMinScore=5000 -chainLinearGap=loose \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > do.log 2>&1
    # real    577m9.861s

    cat fb.hg38.chainColLiv1Link.txt
    # 143694750 bases of 3049335806 (4.712%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` hg38 colLiv1) > rbest.log 2>&1 &
    # real    39m12.952s

    # and for the swap:
    mkdir /hive/data/genomes/colLiv1/bed/blastz.hg38.swap
    cd /hive/data/genomes/colLiv1/bed/blastz.hg38.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/hg38/bed/lastzColLiv1.2015-02-13/DEF \
        -swap -chainMinScore=5000 -chainLinearGap=loose \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    #  real    17m12.980s

    cat fb.colLiv1.chainHg38Link.txt
    # 111080887 bases of 1086925875 (10.220%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` colLiv1 hg38) > rbest.log 2>&1
    # real    57m22.697s

#########################################################################
# LASTZ human/hg38 vs. chicken/galGal4 - (DONE - 2015-02-13 - Hiram)
    mkdir /hive/data/genomes/hg38/bed/lastzGalGal4.2015-02-13
    cd /hive/data/genomes/hg38/bed/lastzGalGal4.2015-02-13

    cat << '_EOF_' > DEF
# human vs chicken
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.54/bin/lastz
BLASTZ_O=400
BLASTZ_E=30
BLASTZ_Y=3400
BLASTZ_L=6000
BLASTZ_K=2200
BLASTZ_M=50
BLASTZ_Q=/scratch/data/blastz/HoxD55.q
#      A    C    G    T
#     91  -90  -25 -100
#    -90  100 -100  -25
#    -25 -100  100  -90
#   -100  -25  -90  91

# TARGET: human hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CTGDIR=/hive/data/genomes/hg38/hg38.contigs.2bit
SEQ1_CTGLEN=/hive/data/genomes/hg38/hg38.contigs.chrom.sizes
SEQ1_LIFT=/hive/data/genomes/hg38/jkStuff/hg38.contigs.lift
SEQ1_CHUNK=40000000
SEQ1_LIMIT=30
SEQ1_LAP=10000

# QUERY: chicken galGal4
SEQ2_DIR=/hive/data/genomes/galGal4/galGal4.2bit
SEQ2_LEN=/hive/data/genomes/galGal4/chrom.sizes
SEQ2_CHUNK=20000000
SEQ2_LIMIT=30
SEQ2_LAP=0

BASE=/hive/data/genomes/hg38/bed/lastzGalGal4.2015-02-13
TMPDIR=/dev/shm
'_EOF_'
    # << happy emacs

    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
        -chainMinScore=5000 -chainLinearGap=loose \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > do.log 2>&1
    # real    591m53.978s

    cat fb.hg38.chainGalGal4Link.txt
    # 143193682 bases of 3049335806 (4.696%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` hg38 galGal4) > rbest.log 2>&1 &
    # real    22m9.725s

    # and for the swap:
    mkdir /hive/data/genomes/galGal4/bed/blastz.hg38.swap
    cd /hive/data/genomes/galGal4/bed/blastz.hg38.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/hg38/bed/lastzGalGal4.2015-02-13/DEF \
        -swap -chainMinScore=5000 -chainLinearGap=loose \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    #  real    19m26.680s

    cat fb.galGal4.chainHg38Link.txt
    # 112454237 bases of 1032854810 (10.888%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` galGal4 hg38) > rbest.log 2>&1
    # real    16m49.158s

#########################################################################
# LASTZ human/hg38 vs. Mallard duck/anaPla1 - (DONE - 2015-02-13 - Hiram)
    mkdir /hive/data/genomes/hg38/bed/lastzAnaPla1.2015-02-13
    cd /hive/data/genomes/hg38/bed/lastzAnaPla1.2015-02-13

    cat << '_EOF_' > DEF
# human vs Mallard duck
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.54/bin/lastz
BLASTZ_O=400
BLASTZ_E=30
BLASTZ_Y=3400
BLASTZ_L=6000
BLASTZ_K=2200
BLASTZ_M=50
BLASTZ_Q=/scratch/data/blastz/HoxD55.q
#      A    C    G    T
#     91  -90  -25 -100
#    -90  100 -100  -25
#    -25 -100  100  -90
#   -100  -25  -90  91

# TARGET: human hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CTGDIR=/hive/data/genomes/hg38/hg38.contigs.2bit
SEQ1_CTGLEN=/hive/data/genomes/hg38/hg38.contigs.chrom.sizes
SEQ1_LIFT=/hive/data/genomes/hg38/jkStuff/hg38.contigs.lift
SEQ1_CHUNK=40000000
SEQ1_LIMIT=30
SEQ1_LAP=10000

# QUERY: Mallard duck anaPla1
SEQ2_DIR=/hive/data/genomes/anaPla1/anaPla1.2bit
SEQ2_LEN=/hive/data/genomes/anaPla1/chrom.sizes
SEQ2_CHUNK=20000000
SEQ2_LIMIT=200
SEQ2_LAP=0

BASE=/hive/data/genomes/hg38/bed/lastzAnaPla1.2015-02-13
TMPDIR=/dev/shm
'_EOF_'
    # << happy emacs

    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
        -chainMinScore=5000 -chainLinearGap=loose \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > do.log 2>&1
    # real    548m49.861s

    cat fb.hg38.chainAnaPla1Link.txt
    # 130130831 bases of 3049335806 (4.268%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` hg38 anaPla1) > rbest.log 2>&1 &
    # real    40m39.914s

    # and for the swap:
    mkdir /hive/data/genomes/anaPla1/bed/blastz.hg38.swap
    cd /hive/data/genomes/anaPla1/bed/blastz.hg38.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/hg38/bed/lastzAnaPla1.2015-02-13/DEF \
        -swap -chainMinScore=5000 -chainLinearGap=loose \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    #  real    18m52.863s

    cat fb.anaPla1.chainHg38Link.txt
    # 103561071 bases of 1069972754 (9.679%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` anaPla1 hg38) > rbest.log 2>&1
    # real    68m35.285s

#########################################################################
# LASTZ human/hg38 vs. turkey/melGal1 - (DONE - 2015-02-13 - Hiram)
    mkdir /hive/data/genomes/hg38/bed/lastzMelGal1.2015-02-13
    cd /hive/data/genomes/hg38/bed/lastzMelGal1.2015-02-13

    cat << '_EOF_' > DEF
# human vs turkey
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.54/bin/lastz
BLASTZ_O=400
BLASTZ_E=30
BLASTZ_Y=3400
BLASTZ_L=6000
BLASTZ_K=2200
BLASTZ_M=50
BLASTZ_Q=/scratch/data/blastz/HoxD55.q
#      A    C    G    T
#     91  -90  -25 -100
#    -90  100 -100  -25
#    -25 -100  100  -90
#   -100  -25  -90  91

# TARGET: human hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CTGDIR=/hive/data/genomes/hg38/hg38.contigs.2bit
SEQ1_CTGLEN=/hive/data/genomes/hg38/hg38.contigs.chrom.sizes
SEQ1_LIFT=/hive/data/genomes/hg38/jkStuff/hg38.contigs.lift
SEQ1_CHUNK=40000000
SEQ1_LIMIT=30
SEQ1_LAP=10000

# QUERY: turkey melGal1
SEQ2_DIR=/hive/data/genomes/melGal1/melGal1.2bit
SEQ2_LEN=/hive/data/genomes/melGal1/chrom.sizes
SEQ2_CHUNK=20000000
SEQ2_LIMIT=30
SEQ2_LAP=0

BASE=/hive/data/genomes/hg38/bed/lastzMelGal1.2015-02-13
TMPDIR=/dev/shm
'_EOF_'
    # << happy emacs

    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
        -chainMinScore=5000 -chainLinearGap=loose \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > do.log 2>&1
    # real    655m4.317s

    cat fb.hg38.chainMelGal1Link.txt
    # 131975070 bases of 3049335806 (4.328%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` hg38 melGal1) > rbest.log 2>&1 &
    # real    14m2.560s

    # and for the swap:
    mkdir /hive/data/genomes/melGal1/bed/blastz.hg38.swap
    cd /hive/data/genomes/melGal1/bed/blastz.hg38.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/hg38/bed/lastzMelGal1.2015-02-13/DEF \
        -swap -chainMinScore=5000 -chainLinearGap=loose \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    #  real    12m24.021s

    cat fb.melGal1.chainHg38Link.txt
    # 102272881 bases of 935922386 (10.927%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` melGal1 hg38) > rbest.log 2>&1
    # real    7m21.946s

#########################################################################
# LASTZ human/hg38 vs. Saker falcon/falChe1 - (DONE - 2015-02-13 - Hiram)
    mkdir /hive/data/genomes/hg38/bed/lastzFalChe1.2015-02-13
    cd /hive/data/genomes/hg38/bed/lastzFalChe1.2015-02-13

    cat << '_EOF_' > DEF
# human vs Saker falcon
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.54/bin/lastz
BLASTZ_O=400
BLASTZ_E=30
BLASTZ_Y=3400
BLASTZ_L=6000
BLASTZ_K=2200
BLASTZ_M=50
BLASTZ_Q=/scratch/data/blastz/HoxD55.q
#      A    C    G    T
#     91  -90  -25 -100
#    -90  100 -100  -25
#    -25 -100  100  -90
#   -100  -25  -90  91

# TARGET: human hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CTGDIR=/hive/data/genomes/hg38/hg38.contigs.2bit
SEQ1_CTGLEN=/hive/data/genomes/hg38/hg38.contigs.chrom.sizes
SEQ1_LIFT=/hive/data/genomes/hg38/jkStuff/hg38.contigs.lift
SEQ1_CHUNK=40000000
SEQ1_LIMIT=30
SEQ1_LAP=10000

# QUERY: Saker falcon falChe1
SEQ2_DIR=/hive/data/genomes/falChe1/falChe1.2bit
SEQ2_LEN=/hive/data/genomes/falChe1/chrom.sizes
SEQ2_CHUNK=20000000
SEQ2_LIMIT=30
SEQ2_LAP=0

BASE=/hive/data/genomes/hg38/bed/lastzFalChe1.2015-02-13
TMPDIR=/dev/shm
'_EOF_'
    # << happy emacs

    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
        -chainMinScore=5000 -chainLinearGap=loose \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > do.log 2>&1
    # real    542m16.464s

    cat fb.hg38.chainFalChe1Link.txt
    # 147225031 bases of 3049335806 (4.828%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` hg38 falChe1) > rbest.log 2>&1 &
    # real    8m23.849s

    # and for the swap:
    mkdir /hive/data/genomes/falChe1/bed/blastz.hg38.swap
    cd /hive/data/genomes/falChe1/bed/blastz.hg38.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/hg38/bed/lastzFalChe1.2015-02-13/DEF \
        -swap -chainMinScore=5000 -chainLinearGap=loose \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    #  real    14m3.049s

    cat fb.falChe1.chainHg38Link.txt
    # 113693444 bases of 1150993769 (9.878%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` falChe1 hg38) > rbest.log 2>&1
    # real    18m4.600s

#########################################################################
# LASTZ human/hg38 vs. Peregrine falcon/falPer1 - (DONE - 2015-02-13 - Hiram)
    mkdir /hive/data/genomes/hg38/bed/lastzFalPer1.2015-02-13
    cd /hive/data/genomes/hg38/bed/lastzFalPer1.2015-02-13

    cat << '_EOF_' > DEF
# human vs Peregrine falcon
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.54/bin/lastz
BLASTZ_O=400
BLASTZ_E=30
BLASTZ_Y=3400
BLASTZ_L=6000
BLASTZ_K=2200
BLASTZ_M=50
BLASTZ_Q=/scratch/data/blastz/HoxD55.q
#      A    C    G    T
#     91  -90  -25 -100
#    -90  100 -100  -25
#    -25 -100  100  -90
#   -100  -25  -90  91

# TARGET: human hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CTGDIR=/hive/data/genomes/hg38/hg38.contigs.2bit
SEQ1_CTGLEN=/hive/data/genomes/hg38/hg38.contigs.chrom.sizes
SEQ1_LIFT=/hive/data/genomes/hg38/jkStuff/hg38.contigs.lift
SEQ1_CHUNK=40000000
SEQ1_LIMIT=30
SEQ1_LAP=10000

# QUERY: Peregrine falcon falPer1
SEQ2_DIR=/hive/data/genomes/falPer1/falPer1.2bit
SEQ2_LEN=/hive/data/genomes/falPer1/chrom.sizes
SEQ2_CHUNK=20000000
SEQ2_LIMIT=30
SEQ2_LAP=0

BASE=/hive/data/genomes/hg38/bed/lastzFalPer1.2015-02-13
TMPDIR=/dev/shm
'_EOF_'
    # << happy emacs

    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
        -chainMinScore=5000 -chainLinearGap=loose \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > do.log 2>&1
    # real    551m19.392s

    cat fb.hg38.chainFalPer1Link.txt
    # 150205756 bases of 3049335806 (4.926%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` hg38 falPer1) > rbest.log 2>&1 &
    # real    6m7.675s

    # and for the swap:
    mkdir /hive/data/genomes/falPer1/bed/blastz.hg38.swap
    cd /hive/data/genomes/falPer1/bed/blastz.hg38.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/hg38/bed/lastzFalPer1.2015-02-13/DEF \
        -swap -chainMinScore=5000 -chainLinearGap=loose \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    #  real    14m47.580s

    cat fb.falPer1.chainHg38Link.txt
    # 115649151 bases of 1153404357 (10.027%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` falPer1 hg38) > rbest.log 2>&1
    # real    25m36.021s

#########################################################################
# LASTZ human/hg38 vs. parrot/amaVit1 - (DONE - 2015-02-13 - Hiram)
    mkdir /hive/data/genomes/hg38/bed/lastzAmaVit1.2015-02-13
    cd /hive/data/genomes/hg38/bed/lastzAmaVit1.2015-02-13

    cat << '_EOF_' > DEF
# human vs parrot
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.54/bin/lastz
BLASTZ_O=400
BLASTZ_E=30
BLASTZ_Y=3400
BLASTZ_L=6000
BLASTZ_K=2200
BLASTZ_M=50
BLASTZ_Q=/scratch/data/blastz/HoxD55.q
#      A    C    G    T
#     91  -90  -25 -100
#    -90  100 -100  -25
#    -25 -100  100  -90
#   -100  -25  -90  91

# TARGET: human hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CTGDIR=/hive/data/genomes/hg38/hg38.contigs.2bit
SEQ1_CTGLEN=/hive/data/genomes/hg38/hg38.contigs.chrom.sizes
SEQ1_LIFT=/hive/data/genomes/hg38/jkStuff/hg38.contigs.lift
SEQ1_CHUNK=40000000
SEQ1_LIMIT=30
SEQ1_LAP=10000

# QUERY: parrot amaVit1
SEQ2_DIR=/hive/data/genomes/amaVit1/amaVit1.2bit
SEQ2_LEN=/hive/data/genomes/amaVit1/chrom.sizes
SEQ2_CHUNK=20000000
SEQ2_LIMIT=200
SEQ2_LAP=0

BASE=/hive/data/genomes/hg38/bed/lastzAmaVit1.2015-02-13
TMPDIR=/dev/shm
'_EOF_'
    # << happy emacs

    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
        -chainMinScore=5000 -chainLinearGap=loose \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > do.log 2>&1
    # real    657m27.659s

    cat fb.hg38.chainAmaVit1Link.txt
    # 127630825 bases of 3049335806 (4.186%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` hg38 amaVit1) > rbest.log 2>&1 &
    # real    9m2.061s

    # and for the swap:
    mkdir /hive/data/genomes/amaVit1/bed/blastz.hg38.swap
    cd /hive/data/genomes/amaVit1/bed/blastz.hg38.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/hg38/bed/lastzAmaVit1.2015-02-13/DEF \
        -swap -chainMinScore=5000 -chainLinearGap=loose \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    #  real    76m6.072s

    cat fb.amaVit1.chainHg38Link.txt
    # 106957200 bases of 1128255752 (9.480%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` amaVit1 hg38) > rbest.log 2>&1
    # real    107m34.617s

#########################################################################
# LASTZ human/hg38 vs. Scarlet macaw/araMac1 - (DONE - 2015-02-17 - Hiram)
    mkdir /hive/data/genomes/hg38/bed/lastzAraMac1.2015-02-17
    cd /hive/data/genomes/hg38/bed/lastzAraMac1.2015-02-17

    cat << '_EOF_' > DEF
# human vs Scarlet macaw
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.54/bin/lastz
BLASTZ_O=400
BLASTZ_E=30
BLASTZ_Y=3400
BLASTZ_L=6000
BLASTZ_K=2200
BLASTZ_M=50
BLASTZ_Q=/scratch/data/blastz/HoxD55.q
#      A    C    G    T
#     91  -90  -25 -100
#    -90  100 -100  -25
#    -25 -100  100  -90
#   -100  -25  -90  91

# TARGET: human hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CTGDIR=/hive/data/genomes/hg38/hg38.contigs.2bit
SEQ1_CTGLEN=/hive/data/genomes/hg38/hg38.contigs.chrom.sizes
SEQ1_LIFT=/hive/data/genomes/hg38/jkStuff/hg38.contigs.lift
SEQ1_CHUNK=40000000
SEQ1_LIMIT=30
SEQ1_LAP=10000

# QUERY: Scarlet macaw araMac1
SEQ2_DIR=/hive/data/genomes/araMac1/araMac1.2bit
SEQ2_LEN=/hive/data/genomes/araMac1/chrom.sizes
SEQ2_CHUNK=20000000
SEQ2_LIMIT=200
SEQ2_LAP=0

BASE=/hive/data/genomes/hg38/bed/lastzAraMac1.2015-02-17
TMPDIR=/dev/shm
'_EOF_'
    # << happy emacs

    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
        -chainMinScore=5000 -chainLinearGap=loose \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > do.log 2>&1
    # real    246m48.471s

    cat fb.hg38.chainAraMac1Link.txt
    # 115478631 bases of 3049335806 (3.787%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` hg38 araMac1) > rbest.log 2>&1 &
    # real    9m59.145s   # lost rbest.log

    # and for the swap:
    mkdir /hive/data/genomes/araMac1/bed/blastz.hg38.swap
    cd /hive/data/genomes/araMac1/bed/blastz.hg38.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/hg38/bed/lastzAraMac1.2015-02-17/DEF \
        -swap -chainMinScore=5000 -chainLinearGap=loose \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    #  real    70m16.338s

    cat fb.araMac1.chainHg38Link.txt
    # 90173740 bases of 997636166 (9.039%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` araMac1 hg38) > rbest.log 2>&1
    # real    42m44.255s

#########################################################################
# LASTZ human/hg38 vs. Tibetan ground jay/pseHum1 - (DONE - 2015-02-17 - Hiram)
    mkdir /hive/data/genomes/hg38/bed/lastzPseHum1.2015-02-17
    cd /hive/data/genomes/hg38/bed/lastzPseHum1.2015-02-17

    cat << '_EOF_' > DEF
# human vs Tibetan ground jay
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.54/bin/lastz
BLASTZ_O=400
BLASTZ_E=30
BLASTZ_Y=3400
BLASTZ_L=6000
BLASTZ_K=2200
BLASTZ_M=50
BLASTZ_Q=/scratch/data/blastz/HoxD55.q
#      A    C    G    T
#     91  -90  -25 -100
#    -90  100 -100  -25
#    -25 -100  100  -90
#   -100  -25  -90  91

# TARGET: human hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CTGDIR=/hive/data/genomes/hg38/hg38.contigs.2bit
SEQ1_CTGLEN=/hive/data/genomes/hg38/hg38.contigs.chrom.sizes
SEQ1_LIFT=/hive/data/genomes/hg38/jkStuff/hg38.contigs.lift
SEQ1_CHUNK=40000000
SEQ1_LIMIT=30
SEQ1_LAP=10000

# QUERY: Tibetan ground jay pseHum1
SEQ2_DIR=/hive/data/genomes/pseHum1/pseHum1.2bit
SEQ2_LEN=/hive/data/genomes/pseHum1/chrom.sizes
SEQ2_CHUNK=20000000
SEQ2_LIMIT=30
SEQ2_LAP=0

BASE=/hive/data/genomes/hg38/bed/lastzPseHum1.2015-02-17
TMPDIR=/dev/shm
'_EOF_'
    # << happy emacs

    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
        -chainMinScore=5000 -chainLinearGap=loose \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > do.log 2>&1
    # real    70m22.110s
    # continuing after cluster trouble:
    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
        -chainMinScore=5000 -chainLinearGap=loose \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -continue=cat -syntenicNet) > cat.log 2>&1
    # real    34m11.495s

    cat fb.hg38.chainPseHum1Link.txt
    # 156923153 bases of 3049335806 (5.146%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` hg38 pseHum1) \
       > rbest.log 2>&1 &
    # real    11m52.623s

    # and for the swap:
    mkdir /hive/data/genomes/pseHum1/bed/blastz.hg38.swap
    cd /hive/data/genomes/pseHum1/bed/blastz.hg38.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/hg38/bed/lastzPseHum1.2015-02-17/DEF \
        -swap -chainMinScore=5000 -chainLinearGap=loose \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    #  real    14m38.524s

    cat fb.pseHum1.chainHg38Link.txt
    # 122950927 bases of 1030030436 (11.937%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` pseHum1 hg38) \
       > rbest.log 2>&1
    # real    11m38.841s

#########################################################################
# LASTZ human/hg38 vs. budgerigar/melUnd1 - (DONE - 2015-02-17 - Hiram)
    mkdir /hive/data/genomes/hg38/bed/lastzMelUnd1.2015-02-17
    cd /hive/data/genomes/hg38/bed/lastzMelUnd1.2015-02-17

    cat << '_EOF_' > DEF
# human vs budgerigar
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.54/bin/lastz
BLASTZ_O=400
BLASTZ_E=30
BLASTZ_Y=3400
BLASTZ_L=6000
BLASTZ_K=2200
BLASTZ_M=50
BLASTZ_Q=/scratch/data/blastz/HoxD55.q
#      A    C    G    T
#     91  -90  -25 -100
#    -90  100 -100  -25
#    -25 -100  100  -90
#   -100  -25  -90  91

# TARGET: human hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CTGDIR=/hive/data/genomes/hg38/hg38.contigs.2bit
SEQ1_CTGLEN=/hive/data/genomes/hg38/hg38.contigs.chrom.sizes
SEQ1_LIFT=/hive/data/genomes/hg38/jkStuff/hg38.contigs.lift
SEQ1_CHUNK=40000000
SEQ1_LIMIT=30
SEQ1_LAP=10000

# QUERY: budgerigar melUnd1
SEQ2_DIR=/hive/data/genomes/melUnd1/melUnd1.2bit
SEQ2_LEN=/hive/data/genomes/melUnd1/chrom.sizes
SEQ2_CHUNK=20000000
SEQ2_LIMIT=30
SEQ2_LAP=0

BASE=/hive/data/genomes/hg38/bed/lastzMelUnd1.2015-02-17
TMPDIR=/dev/shm
'_EOF_'
    # << happy emacs

    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
        -chainMinScore=5000 -chainLinearGap=loose \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > do.log 2>&1
    # real    2082m35.909s

    cat fb.hg38.chainMelUnd1Link.txt
    # 136423508 bases of 3049335806 (4.474%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` hg38 melUnd1) \
       > rbest.log 2>&1 &
    # real    9m33.306s

    # and for the swap:
    mkdir /hive/data/genomes/melUnd1/bed/blastz.hg38.swap
    cd /hive/data/genomes/melUnd1/bed/blastz.hg38.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/hg38/bed/lastzMelUnd1.2015-02-17/DEF \
        -swap -chainMinScore=5000 -chainLinearGap=loose \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    #  real    12m38.168s

    cat fb.melUnd1.chainHg38Link.txt
    # 107164699 bases of 1086614815 (9.862%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` melUnd1 hg38) \
       > rbest.log 2>&1
    # real    9m40.749s

#########################################################################
# LASTZ human/hg38 vs. Collard flycatcher/ficAlb2 - (DONE - 2015-02-17 - Hiram)
    mkdir /hive/data/genomes/hg38/bed/lastzFicAlb2.2015-02-17
    cd /hive/data/genomes/hg38/bed/lastzFicAlb2.2015-02-17

    cat << '_EOF_' > DEF
# human vs Collard flycatcher
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.54/bin/lastz
BLASTZ_O=400
BLASTZ_E=30
BLASTZ_Y=3400
BLASTZ_L=6000
BLASTZ_K=2200
BLASTZ_M=50
BLASTZ_Q=/scratch/data/blastz/HoxD55.q
#      A    C    G    T
#     91  -90  -25 -100
#    -90  100 -100  -25
#    -25 -100  100  -90
#   -100  -25  -90  91

# TARGET: human hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CTGDIR=/hive/data/genomes/hg38/hg38.contigs.2bit
SEQ1_CTGLEN=/hive/data/genomes/hg38/hg38.contigs.chrom.sizes
SEQ1_LIFT=/hive/data/genomes/hg38/jkStuff/hg38.contigs.lift
SEQ1_CHUNK=40000000
SEQ1_LIMIT=30
SEQ1_LAP=10000

# QUERY: Collard flycatcher ficAlb2
SEQ2_DIR=/hive/data/genomes/ficAlb2/ficAlb2.2bit
SEQ2_LEN=/hive/data/genomes/ficAlb2/chrom.sizes
SEQ2_CHUNK=20000000
SEQ2_LIMIT=30
SEQ2_LAP=0

BASE=/hive/data/genomes/hg38/bed/lastzFicAlb2.2015-02-17
TMPDIR=/dev/shm
'_EOF_'
    # << happy emacs

    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
        -chainMinScore=5000 -chainLinearGap=loose \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > do.log 2>&1
    # real    1978m13.358s

    cat fb.hg38.chainFicAlb2Link.txt
    # 147048785 bases of 3049335806 (4.822%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` hg38 ficAlb2) > rbest.log 2>&1 &
    # real    10m49.556s

    # and for the swap:
    mkdir /hive/data/genomes/ficAlb2/bed/blastz.hg38.swap
    cd /hive/data/genomes/ficAlb2/bed/blastz.hg38.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/hg38/bed/lastzFicAlb2.2015-02-17/DEF \
        -swap -chainMinScore=5000 -chainLinearGap=loose \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    #  real    15m26.251s

    cat fb.ficAlb2.chainHg38Link.txt
    # 118476285 bases of 1102325870 (10.748%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` ficAlb2 hg38) \
        > rbest.log 2>&1
    # real    12m43.894s

#########################################################################
# LASTZ human/hg38 vs. White throaqted sparrow/zonAlb1 - (DONE - 2015-02-17 - Hiram)
    mkdir /hive/data/genomes/hg38/bed/lastzZonAlb1.2015-02-17
    cd /hive/data/genomes/hg38/bed/lastzZonAlb1.2015-02-17

    cat << '_EOF_' > DEF
# human vs White throaqted sparrow
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.54/bin/lastz
BLASTZ_O=400
BLASTZ_E=30
BLASTZ_Y=3400
BLASTZ_L=6000
BLASTZ_K=2200
BLASTZ_M=50
BLASTZ_Q=/scratch/data/blastz/HoxD55.q
#      A    C    G    T
#     91  -90  -25 -100
#    -90  100 -100  -25
#    -25 -100  100  -90
#   -100  -25  -90  91

# TARGET: human hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CTGDIR=/hive/data/genomes/hg38/hg38.contigs.2bit
SEQ1_CTGLEN=/hive/data/genomes/hg38/hg38.contigs.chrom.sizes
SEQ1_LIFT=/hive/data/genomes/hg38/jkStuff/hg38.contigs.lift
SEQ1_CHUNK=40000000
SEQ1_LIMIT=30
SEQ1_LAP=10000

# QUERY: White throaqted sparrow zonAlb1
SEQ2_DIR=/hive/data/genomes/zonAlb1/zonAlb1.2bit
SEQ2_LEN=/hive/data/genomes/zonAlb1/chrom.sizes
SEQ2_CHUNK=20000000
SEQ2_LIMIT=30
SEQ2_LAP=0

BASE=/hive/data/genomes/hg38/bed/lastzZonAlb1.2015-02-17
TMPDIR=/dev/shm
'_EOF_'
    # << happy emacs

    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
        -chainMinScore=5000 -chainLinearGap=loose \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > do.log 2>&1
    # real    1615m23.324s

    cat fb.hg38.chainZonAlb1Link.txt
    # 137040575 bases of 3049335806 (4.494%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` hg38 zonAlb1) > rbest.log 2>&1 &
    # real    6m4.340s

    # and for the swap:
    mkdir /hive/data/genomes/zonAlb1/bed/blastz.hg38.swap
    cd /hive/data/genomes/zonAlb1/bed/blastz.hg38.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/hg38/bed/lastzZonAlb1.2015-02-17/DEF \
        -swap -chainMinScore=5000 -chainLinearGap=loose \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    #  real    12m59.040s

    cat fb.zonAlb1.chainHg38Link.txt
    # 106367271 bases of 1006303327 (10.570%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` zonAlb1 hg38) > rbest.log 2>&1
    # real    6m51.403s

#########################################################################
# LASTZ human/hg38 vs. Medium ground finch/geoFor1 - (DONE - 2015-02-17 - Hiram)
    mkdir /hive/data/genomes/hg38/bed/lastzGeoFor1.2015-02-17
    cd /hive/data/genomes/hg38/bed/lastzGeoFor1.2015-02-17

    cat << '_EOF_' > DEF
# human vs Medium ground finch
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.54/bin/lastz
BLASTZ_O=400
BLASTZ_E=30
BLASTZ_Y=3400
BLASTZ_L=6000
BLASTZ_K=2200
BLASTZ_M=50
BLASTZ_Q=/scratch/data/blastz/HoxD55.q
#      A    C    G    T
#     91  -90  -25 -100
#    -90  100 -100  -25
#    -25 -100  100  -90
#   -100  -25  -90  91

# TARGET: human hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CTGDIR=/hive/data/genomes/hg38/hg38.contigs.2bit
SEQ1_CTGLEN=/hive/data/genomes/hg38/hg38.contigs.chrom.sizes
SEQ1_LIFT=/hive/data/genomes/hg38/jkStuff/hg38.contigs.lift
SEQ1_CHUNK=40000000
SEQ1_LIMIT=30
SEQ1_LAP=10000

# QUERY: Medium ground finch geoFor1
SEQ2_DIR=/hive/data/genomes/geoFor1/geoFor1.2bit
SEQ2_LEN=/hive/data/genomes/geoFor1/chrom.sizes
SEQ2_CHUNK=20000000
SEQ2_LIMIT=30
SEQ2_LAP=0

BASE=/hive/data/genomes/hg38/bed/lastzGeoFor1.2015-02-17
TMPDIR=/dev/shm
'_EOF_'
    # << happy emacs

    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
        -chainMinScore=5000 -chainLinearGap=loose \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > do.log 2>&1
    # real    2097m14.874s

    cat fb.hg38.chainGeoFor1Link.txt
    # 135529241 bases of 3049335806 (4.445%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` hg38 geoFor1) \
       > rbest.log 2>&1 &
    # real    9m9.547s

    # and for the swap:
    mkdir /hive/data/genomes/geoFor1/bed/blastz.hg38.swap
    cd /hive/data/genomes/geoFor1/bed/blastz.hg38.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/hg38/bed/lastzGeoFor1.2015-02-17/DEF \
        -swap -chainMinScore=5000 -chainLinearGap=loose \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    #  real    13m19.205s

    cat fb.geoFor1.chainHg38Link.txt
    # 107944681 bases of 1041286029 (10.366%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` geoFor1 hg38) \
       > rbest.log 2>&1
    # real    9m35.765s

#########################################################################
# LASTZ human/hg38 vs. Zebra finch/taeGut2 - (DONE - 2015-02-17 - Hiram)
    mkdir /hive/data/genomes/hg38/bed/lastzTaeGut2.2015-02-17
    cd /hive/data/genomes/hg38/bed/lastzTaeGut2.2015-02-17

    cat << '_EOF_' > DEF
# human vs Zebra finch
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.54/bin/lastz
BLASTZ_O=400
BLASTZ_E=30
BLASTZ_Y=3400
BLASTZ_L=6000
BLASTZ_K=2200
BLASTZ_M=50
BLASTZ_Q=/scratch/data/blastz/HoxD55.q
#      A    C    G    T
#     91  -90  -25 -100
#    -90  100 -100  -25
#    -25 -100  100  -90
#   -100  -25  -90  91

# TARGET: human hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CTGDIR=/hive/data/genomes/hg38/hg38.contigs.2bit
SEQ1_CTGLEN=/hive/data/genomes/hg38/hg38.contigs.chrom.sizes
SEQ1_LIFT=/hive/data/genomes/hg38/jkStuff/hg38.contigs.lift
SEQ1_CHUNK=40000000
SEQ1_LIMIT=30
SEQ1_LAP=10000

# QUERY: Zebra finch taeGut2
SEQ2_DIR=/hive/data/genomes/taeGut2/taeGut2.2bit
SEQ2_LEN=/hive/data/genomes/taeGut2/chrom.sizes
SEQ2_CHUNK=20000000
SEQ2_LIMIT=30
SEQ2_LAP=0

BASE=/hive/data/genomes/hg38/bed/lastzTaeGut2.2015-02-17
TMPDIR=/dev/shm
'_EOF_'
    # << happy emacs

    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
        -chainMinScore=5000 -chainLinearGap=loose \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > do.log 2>&1
    # real    3301m5.574s

    cat fb.hg38.chainTaeGut2Link.txt
    # 179692554 bases of 3049335806 (5.893%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` hg38 taeGut2) \
       > rbest.log 2>&1 &
    # real    14m16.442s

    # and for the swap:
    mkdir /hive/data/genomes/taeGut2/bed/blastz.hg38.swap
    cd /hive/data/genomes/taeGut2/bed/blastz.hg38.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/hg38/bed/lastzTaeGut2.2015-02-17/DEF \
        -swap -chainMinScore=5000 -chainLinearGap=loose \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    #  real    37m48.256s

    cat fb.taeGut2.chainHg38Link.txt
    # 151099393 bases of 1222864691 (12.356%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` taeGut2 hg38) \
       > rbest.log 2>&1
    # real    20m21.580s

#########################################################################
# LASTZ human/hg38 vs. Atlantic cod/gadMor1 - (DONE - 2015-02-17 - Hiram)
    mkdir /hive/data/genomes/hg38/bed/lastzGadMor1.2015-02-17
    cd /hive/data/genomes/hg38/bed/lastzGadMor1.2015-02-17

    cat << '_EOF_' > DEF
# human vs Atlantic cod
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.54/bin/lastz
BLASTZ_O=400
BLASTZ_E=30
BLASTZ_Y=3400
BLASTZ_L=6000
BLASTZ_K=2200
BLASTZ_M=50
BLASTZ_Q=/scratch/data/blastz/HoxD55.q
#      A    C    G    T
#     91  -90  -25 -100
#    -90  100 -100  -25
#    -25 -100  100  -90
#   -100  -25  -90  91

# TARGET: human hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CTGDIR=/hive/data/genomes/hg38/hg38.contigs.2bit
SEQ1_CTGLEN=/hive/data/genomes/hg38/hg38.contigs.chrom.sizes
SEQ1_LIFT=/hive/data/genomes/hg38/jkStuff/hg38.contigs.lift
SEQ1_CHUNK=40000000
SEQ1_LIMIT=30
SEQ1_LAP=10000

# QUERY: Atlantic cod gadMor1
SEQ2_DIR=/hive/data/genomes/gadMor1/gadMor1.2bit
SEQ2_LEN=/hive/data/genomes/gadMor1/chrom.sizes
SEQ2_CHUNK=20000000
SEQ2_LIMIT=500
SEQ2_LAP=0

BASE=/hive/data/genomes/hg38/bed/lastzGadMor1.2015-02-17
TMPDIR=/dev/shm
'_EOF_'
    # << happy emacs

    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
        -chainMinScore=5000 -chainLinearGap=loose \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > do.log 2>&1
    # real    1588m35.829s

    cat fb.hg38.chainGadMor1Link.txt
    # 50624248 bases of 3049335806 (1.660%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` hg38 gadMor1) > rbest.log 2>&1 &
    # real    4m28.029s

    # and for the swap:
    mkdir /hive/data/genomes/gadMor1/bed/blastz.hg38.swap
    cd /hive/data/genomes/gadMor1/bed/blastz.hg38.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/hg38/bed/lastzGadMor1.2015-02-17/DEF \
        -swap -chainMinScore=5000 -chainLinearGap=loose \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    #  real    74m26.591s

    cat fb.gadMor1.chainHg38Link.txt
    # 42019467 bases of 608038597 (6.911%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` gadMor1 hg38) > rbest.log 2>&1
    # real    35m52.207s

#########################################################################
# LASTZ human/hg38 vs. Stickleback/gasAcu1 - (DONE - 2015-02-17 - Hiram)
    mkdir /hive/data/genomes/hg38/bed/lastzGasAcu1.2015-02-17
    cd /hive/data/genomes/hg38/bed/lastzGasAcu1.2015-02-17

    cat << '_EOF_' > DEF
# human vs Stickleback
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.54/bin/lastz
BLASTZ_O=400
BLASTZ_E=30
BLASTZ_Y=3400
BLASTZ_L=6000
BLASTZ_K=2200
BLASTZ_M=50
BLASTZ_Q=/scratch/data/blastz/HoxD55.q
#      A    C    G    T
#     91  -90  -25 -100
#    -90  100 -100  -25
#    -25 -100  100  -90
#   -100  -25  -90  91

# TARGET: human hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CTGDIR=/hive/data/genomes/hg38/hg38.contigs.2bit
SEQ1_CTGLEN=/hive/data/genomes/hg38/hg38.contigs.chrom.sizes
SEQ1_LIFT=/hive/data/genomes/hg38/jkStuff/hg38.contigs.lift
SEQ1_CHUNK=40000000
SEQ1_LIMIT=30
SEQ1_LAP=10000

# QUERY: Stickleback gasAcu1
SEQ2_DIR=/hive/data/genomes/gasAcu1/gasAcu1.2bit
SEQ2_LEN=/hive/data/genomes/gasAcu1/chrom.sizes
SEQ2_CHUNK=20000000
SEQ2_LIMIT=1
SEQ2_LAP=0

BASE=/hive/data/genomes/hg38/bed/lastzGasAcu1.2015-02-17
TMPDIR=/dev/shm
'_EOF_'
    # << happy emacs

    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
        -chainMinScore=5000 -chainLinearGap=loose \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > do.log 2>&1
    # real    1053m23.074s

    cat fb.hg38.chainGasAcu1Link.txt
    # 63437294 bases of 3049335806 (2.080%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` hg38 gasAcu1) > rbest.log 2>&1 &
    # about 6 minutes - lost rbest.log

    # and for the swap:
    mkdir /hive/data/genomes/gasAcu1/bed/blastz.hg38.swap
    cd /hive/data/genomes/gasAcu1/bed/blastz.hg38.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/hg38/bed/lastzGasAcu1.2015-02-17/DEF \
        -swap -chainMinScore=5000 -chainLinearGap=loose \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    #  real    9m14.802s

    cat fb.gasAcu1.chainHg38Link.txt
    # 53397634 bases of 446627861 (11.956%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` gasAcu1 hg38) > rbest.log 2>&1
    # real    10m7.401s

#########################################################################
# LASTZ human/hg38 vs. Nile tilapia/oreNil2 - (DONE - 2015-02-17 - Hiram)
    mkdir /hive/data/genomes/hg38/bed/lastzOreNil2.2015-02-17
    cd /hive/data/genomes/hg38/bed/lastzOreNil2.2015-02-17

    cat << '_EOF_' > DEF
# human vs Nile tilapia
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.54/bin/lastz
BLASTZ_O=400
BLASTZ_E=30
BLASTZ_Y=3400
BLASTZ_L=6000
BLASTZ_K=2200
BLASTZ_M=50
BLASTZ_Q=/scratch/data/blastz/HoxD55.q
#      A    C    G    T
#     91  -90  -25 -100
#    -90  100 -100  -25
#    -25 -100  100  -90
#   -100  -25  -90  91

# TARGET: human hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CTGDIR=/hive/data/genomes/hg38/hg38.contigs.2bit
SEQ1_CTGLEN=/hive/data/genomes/hg38/hg38.contigs.chrom.sizes
SEQ1_LIFT=/hive/data/genomes/hg38/jkStuff/hg38.contigs.lift
SEQ1_CHUNK=40000000
SEQ1_LIMIT=30
SEQ1_LAP=10000

# QUERY: Nile tilapia oreNil2
SEQ2_DIR=/hive/data/genomes/oreNil2/oreNil2.2bit
SEQ2_LEN=/hive/data/genomes/oreNil2/chrom.sizes
SEQ2_CHUNK=20000000
SEQ2_LIMIT=20
SEQ2_LAP=0

BASE=/hive/data/genomes/hg38/bed/lastzOreNil2.2015-02-17
TMPDIR=/dev/shm
'_EOF_'
    # << happy emacs

    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
        -chainMinScore=5000 -chainLinearGap=loose \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > do.log 2>&1
    # real    1380m11.717s

    cat fb.hg38.chainOreNil2Link.txt
    # 56961010 bases of 3049335806 (1.868%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` hg38 oreNil2) \
       > rbest.log 2>&1 &
    # real    8m9.098s

    # and for the swap:
    mkdir /hive/data/genomes/oreNil2/bed/blastz.hg38.swap
    cd /hive/data/genomes/oreNil2/bed/blastz.hg38.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/hg38/bed/lastzOreNil2.2015-02-17/DEF \
        -swap -chainMinScore=5000 -chainLinearGap=loose \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    # real    8m56.062s

    cat fb.oreNil2.chainHg38Link.txt
    # 50933712 bases of 816084674 (6.241%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` oreNil2 hg38) \
       > rbest.log 2>&1
    # real    7m54.354s

#########################################################################
# LASTZ human/hg38 vs. Tetraodon/tetNig2 - (DONE - 2015-02-17 - Hiram)
    mkdir /hive/data/genomes/hg38/bed/lastzTetNig2.2015-02-17
    cd /hive/data/genomes/hg38/bed/lastzTetNig2.2015-02-17

    cat << '_EOF_' > DEF
# human vs Tetraodon
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.54/bin/lastz
BLASTZ_O=400
BLASTZ_E=30
BLASTZ_Y=3400
BLASTZ_L=6000
BLASTZ_K=2200
BLASTZ_M=50
BLASTZ_Q=/scratch/data/blastz/HoxD55.q
#      A    C    G    T
#     91  -90  -25 -100
#    -90  100 -100  -25
#    -25 -100  100  -90
#   -100  -25  -90  91

# TARGET: human hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CTGDIR=/hive/data/genomes/hg38/hg38.contigs.2bit
SEQ1_CTGLEN=/hive/data/genomes/hg38/hg38.contigs.chrom.sizes
SEQ1_LIFT=/hive/data/genomes/hg38/jkStuff/hg38.contigs.lift
SEQ1_CHUNK=40000000
SEQ1_LIMIT=30
SEQ1_LAP=10000

# QUERY: Tetraodon tetNig2
SEQ2_DIR=/hive/data/genomes/tetNig2/tetNig2.2bit
SEQ2_LEN=/hive/data/genomes/tetNig2/chrom.sizes
SEQ2_CHUNK=20000000
SEQ2_LIMIT=1
SEQ2_LAP=0

BASE=/hive/data/genomes/hg38/bed/lastzTetNig2.2015-02-17
TMPDIR=/dev/shm
'_EOF_'
    # << happy emacs

    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
        -chainMinScore=5000 -chainLinearGap=loose \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > do.log 2>&1
    # real    537m38.314s

    cat fb.hg38.chainTetNig2Link.txt
    # 53138885 bases of 3049335806 (1.743%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` hg38 tetNig2) > rbest.log 2>&1 &
    # real    8m12.538s

    # and for the swap:
    mkdir /hive/data/genomes/tetNig2/bed/blastz.hg38.swap
    cd /hive/data/genomes/tetNig2/bed/blastz.hg38.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/hg38/bed/lastzTetNig2.2015-02-17/DEF \
        -swap -chainMinScore=5000 -chainLinearGap=loose \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    #  real    6m31.168s

    cat fb.tetNig2.chainHg38Link.txt
    # 43299390 bases of 302314788 (14.323%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` tetNig2 hg38) > rbest.log 2>&1
    # real    5m5.399s

#########################################################################
# LASTZ human/hg38 vs. Princess of Burundi/neoBri1 - (DONE - 2015-02-17 - Hiram)
    mkdir /hive/data/genomes/hg38/bed/lastzNeoBri1.2015-02-17
    cd /hive/data/genomes/hg38/bed/lastzNeoBri1.2015-02-17

    cat << '_EOF_' > DEF
# human vs Princess of Burundi
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.54/bin/lastz
BLASTZ_O=400
BLASTZ_E=30
BLASTZ_Y=3400
BLASTZ_L=6000
BLASTZ_K=2200
BLASTZ_M=50
BLASTZ_Q=/scratch/data/blastz/HoxD55.q
#      A    C    G    T
#     91  -90  -25 -100
#    -90  100 -100  -25
#    -25 -100  100  -90
#   -100  -25  -90  91

# TARGET: human hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CTGDIR=/hive/data/genomes/hg38/hg38.contigs.2bit
SEQ1_CTGLEN=/hive/data/genomes/hg38/hg38.contigs.chrom.sizes
SEQ1_LIFT=/hive/data/genomes/hg38/jkStuff/hg38.contigs.lift
SEQ1_CHUNK=40000000
SEQ1_LIMIT=30
SEQ1_LAP=10000

# QUERY: Princess of Burundi neoBri1
SEQ2_DIR=/hive/data/genomes/neoBri1/neoBri1.2bit
SEQ2_LEN=/hive/data/genomes/neoBri1/chrom.sizes
SEQ2_CHUNK=20000000
SEQ2_LIMIT=20
SEQ2_LAP=0

BASE=/hive/data/genomes/hg38/bed/lastzNeoBri1.2015-02-17
TMPDIR=/dev/shm
'_EOF_'
    # << happy emacs

    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
        -chainMinScore=5000 -chainLinearGap=loose \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > do.log 2>&1
    # real    1316m55.223s

    cat fb.hg38.chainNeoBri1Link.txt
    # 53868820 bases of 3049335806 (1.767%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` hg38 neoBri1) > rbest.log 2>&1 &
    # real    4m18.813s

    # and for the swap:
    mkdir /hive/data/genomes/neoBri1/bed/blastz.hg38.swap
    cd /hive/data/genomes/neoBri1/bed/blastz.hg38.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/hg38/bed/lastzNeoBri1.2015-02-17/DEF \
        -swap -chainMinScore=5000 -chainLinearGap=loose \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    #  real    8m59.125s

    cat fb.neoBri1.chainHg38Link.txt
    # 46915356 bases of 685897281 (6.840%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` neoBri1 hg38) > rbest.log 2>&1
    # real    6m25.911s

#########################################################################
# LASTZ human/hg38 vs. Yellowbelly pufferfish/takFla1 - (DONE - 2015-02-17 - Hiram)
    mkdir /hive/data/genomes/hg38/bed/lastzTakFla1.2015-02-17
    cd /hive/data/genomes/hg38/bed/lastzTakFla1.2015-02-17

    cat << '_EOF_' > DEF
# human vs Yellowbelly pufferfish
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.54/bin/lastz
BLASTZ_O=400
BLASTZ_E=30
BLASTZ_Y=3400
BLASTZ_L=6000
BLASTZ_K=2200
BLASTZ_M=50
BLASTZ_Q=/scratch/data/blastz/HoxD55.q
#      A    C    G    T
#     91  -90  -25 -100
#    -90  100 -100  -25
#    -25 -100  100  -90
#   -100  -25  -90  91

# TARGET: human hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CTGDIR=/hive/data/genomes/hg38/hg38.contigs.2bit
SEQ1_CTGLEN=/hive/data/genomes/hg38/hg38.contigs.chrom.sizes
SEQ1_LIFT=/hive/data/genomes/hg38/jkStuff/hg38.contigs.lift
SEQ1_CHUNK=40000000
SEQ1_LIMIT=30
SEQ1_LAP=10000

# QUERY: Yellowbelly pufferfish takFla1
SEQ2_DIR=/hive/data/genomes/takFla1/takFla1.2bit
SEQ2_LEN=/hive/data/genomes/takFla1/chrom.sizes
SEQ2_CHUNK=20000000
SEQ2_LIMIT=40
SEQ2_LAP=0

BASE=/hive/data/genomes/hg38/bed/lastzTakFla1.2015-02-17
TMPDIR=/dev/shm
'_EOF_'
    # << happy emacs

    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
        -chainMinScore=5000 -chainLinearGap=loose \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > do.log 2>&1
    # real    1193m52.421s

    cat fb.hg38.chainTakFla1Link.txt
    # 47205001 bases of 3049335806 (1.548%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` hg38 takFla1) > rbest.log 2>&1 &
    # real    2m58.484s

    # and for the swap:
    mkdir /hive/data/genomes/takFla1/bed/blastz.hg38.swap
    cd /hive/data/genomes/takFla1/bed/blastz.hg38.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/hg38/bed/lastzTakFla1.2015-02-17/DEF \
        -swap -chainMinScore=5000 -chainLinearGap=loose \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    #  real    7m24.854s

    cat fb.takFla1.chainHg38Link.txt
    # 35632361 bases of 314848639 (11.317%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` takFla1 hg38) > rbest.log 2>&1
    # real    8m20.901s

#########################################################################
# LASTZ human/hg38 vs. Burton's mouthbreeder/hapBur1 - (DONE - 2015-02-17 - Hiram)
    mkdir /hive/data/genomes/hg38/bed/lastzHapBur1.2015-02-17
    cd /hive/data/genomes/hg38/bed/lastzHapBur1.2015-02-17

    cat << '_EOF_' > DEF
# human vs Burton's mouthbreeder
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.54/bin/lastz
BLASTZ_O=400
BLASTZ_E=30
BLASTZ_Y=3400
BLASTZ_L=6000
BLASTZ_K=2200
BLASTZ_M=50
BLASTZ_Q=/scratch/data/blastz/HoxD55.q
#      A    C    G    T
#     91  -90  -25 -100
#    -90  100 -100  -25
#    -25 -100  100  -90
#   -100  -25  -90  91

# TARGET: human hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CTGDIR=/hive/data/genomes/hg38/hg38.contigs.2bit
SEQ1_CTGLEN=/hive/data/genomes/hg38/hg38.contigs.chrom.sizes
SEQ1_LIFT=/hive/data/genomes/hg38/jkStuff/hg38.contigs.lift
SEQ1_CHUNK=40000000
SEQ1_LIMIT=30
SEQ1_LAP=10000

# QUERY: Burton's mouthbreeder hapBur1
SEQ2_DIR=/hive/data/genomes/hapBur1/hapBur1.2bit
SEQ2_LEN=/hive/data/genomes/hapBur1/chrom.sizes
SEQ2_CHUNK=20000000
SEQ2_LIMIT=20
SEQ2_LAP=0

BASE=/hive/data/genomes/hg38/bed/lastzHapBur1.2015-02-17
TMPDIR=/dev/shm
'_EOF_'
    # << happy emacs

    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
        -chainMinScore=5000 -chainLinearGap=loose \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > do.log 2>&1
    # real    1288m42.717s

    cat fb.hg38.chainHapBur1Link.txt
    # 54379915 bases of 3049335806 (1.783%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` hg38 hapBur1) > rbest.log 2>&1 &
    # real    3m45.453s

    # and for the swap:
    mkdir /hive/data/genomes/hapBur1/bed/blastz.hg38.swap
    cd /hive/data/genomes/hapBur1/bed/blastz.hg38.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/hg38/bed/lastzHapBur1.2015-02-17/DEF \
        -swap -chainMinScore=5000 -chainLinearGap=loose \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    #  real    9m18.063s

    cat fb.hapBur1.chainHg38Link.txt
    # 47956127 bases of 698936397 (6.861%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` hapBur1 hg38) > rbest.log 2>&1
    # real    6m53.796s

#########################################################################
# LASTZ human/hg38 vs. Fugu/fr3 - (DONE - 2015-02-17 - Hiram)
    mkdir /hive/data/genomes/hg38/bed/lastzFr3.2015-02-17
    cd /hive/data/genomes/hg38/bed/lastzFr3.2015-02-17

    cat << '_EOF_' > DEF
# human vs Fugu
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.54/bin/lastz
BLASTZ_O=400
BLASTZ_E=30
BLASTZ_Y=3400
BLASTZ_L=6000
BLASTZ_K=2200
BLASTZ_M=50
BLASTZ_Q=/scratch/data/blastz/HoxD55.q
#      A    C    G    T
#     91  -90  -25 -100
#    -90  100 -100  -25
#    -25 -100  100  -90
#   -100  -25  -90  91

# TARGET: human hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CTGDIR=/hive/data/genomes/hg38/hg38.contigs.2bit
SEQ1_CTGLEN=/hive/data/genomes/hg38/hg38.contigs.chrom.sizes
SEQ1_LIFT=/hive/data/genomes/hg38/jkStuff/hg38.contigs.lift
SEQ1_CHUNK=40000000
SEQ1_LIMIT=30
SEQ1_LAP=10000

# QUERY: Fugu fr3
SEQ2_DIR=/hive/data/genomes/fr3/fr3.2bit
SEQ2_LEN=/hive/data/genomes/fr3/chrom.sizes
SEQ2_CHUNK=20000000
SEQ2_LIMIT=20
SEQ2_LAP=0

BASE=/hive/data/genomes/hg38/bed/lastzFr3.2015-02-17
TMPDIR=/dev/shm
'_EOF_'
    # << happy emacs

    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
        -chainMinScore=5000 -chainLinearGap=loose \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > do.log 2>&1
    # real    906m48.419s

    cat fb.hg38.chainFr3Link.txt
    # 54409247 bases of 3049335806 (1.784%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` hg38 fr3) > rbest.log 2>&1 &
    # real    4m4.720s

    # and for the swap:
    mkdir /hive/data/genomes/fr3/bed/blastz.hg38.swap
    cd /hive/data/genomes/fr3/bed/blastz.hg38.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/hg38/bed/lastzFr3.2015-02-17/DEF \
        -swap -chainMinScore=5000 -chainLinearGap=loose \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    #  real    6m35.968s

    cat fb.fr3.chainHg38Link.txt
    # 43496560 bases of 350961831 (12.394%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` fr3 hg38) > rbest.log 2>&1
    # real    11m12.304s

#########################################################################
# LASTZ human/hg38 vs. Mexican tetra cavefish/astMex1 - (DONE - 2015-02-17 - Hiram)
    mkdir /hive/data/genomes/hg38/bed/lastzAstMex1.2015-02-17
    cd /hive/data/genomes/hg38/bed/lastzAstMex1.2015-02-17

    cat << '_EOF_' > DEF
# human vs Mexican tetra cavefish
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.54/bin/lastz
BLASTZ_O=400
BLASTZ_E=30
BLASTZ_Y=3400
BLASTZ_L=6000
BLASTZ_K=2200
BLASTZ_M=50
BLASTZ_Q=/scratch/data/blastz/HoxD55.q
#      A    C    G    T
#     91  -90  -25 -100
#    -90  100 -100  -25
#    -25 -100  100  -90
#   -100  -25  -90  91

# TARGET: human hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CTGDIR=/hive/data/genomes/hg38/hg38.contigs.2bit
SEQ1_CTGLEN=/hive/data/genomes/hg38/hg38.contigs.chrom.sizes
SEQ1_LIFT=/hive/data/genomes/hg38/jkStuff/hg38.contigs.lift
SEQ1_CHUNK=40000000
SEQ1_LIMIT=30
SEQ1_LAP=10000

# QUERY: Mexican tetra cavefish astMex1
SEQ2_DIR=/hive/data/genomes/astMex1/astMex1.2bit
SEQ2_LEN=/hive/data/genomes/astMex1/chrom.sizes
SEQ2_CHUNK=20000000
SEQ2_LIMIT=20
SEQ2_LAP=0

BASE=/hive/data/genomes/hg38/bed/lastzAstMex1.2015-02-17
TMPDIR=/dev/shm
'_EOF_'
    # << happy emacs

    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
        -chainMinScore=5000 -chainLinearGap=loose \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > do.log 2>&1
    # real    1566m37.808s

    cat fb.hg38.chainAstMex1Link.txt
    # 67854134 bases of 3049335806 (2.225%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` hg38 astMex1) > rbest.log 2>&1 &
    # real    4m58.664s

    # and for the swap:
    mkdir /hive/data/genomes/astMex1/bed/blastz.hg38.swap
    cd /hive/data/genomes/astMex1/bed/blastz.hg38.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/hg38/bed/lastzAstMex1.2015-02-17/DEF \
        -swap -chainMinScore=5000 -chainLinearGap=loose \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    #  real    13m50.072s

    cat fb.astMex1.chainHg38Link.txt
    # 61379040 bases of 964264884 (6.365%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` astMex1 hg38) > rbest.log 2>&1
    # real    6m31.123s

#########################################################################
# LASTZ human/hg38 vs. X. tropicalis/xenTro7 - (DONE - 2015-02-18 - Hiram)
    mkdir /hive/data/genomes/hg38/bed/lastzXenTro7.2015-02-18
    cd /hive/data/genomes/hg38/bed/lastzXenTro7.2015-02-18

    cat << '_EOF_' > DEF
# human vs X. tropicalis
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.54/bin/lastz
BLASTZ_O=400
BLASTZ_E=30
BLASTZ_Y=3400
BLASTZ_L=6000
BLASTZ_K=2200
BLASTZ_M=50
BLASTZ_Q=/scratch/data/blastz/HoxD55.q
#      A    C    G    T
#     91  -90  -25 -100
#    -90  100 -100  -25
#    -25 -100  100  -90
#   -100  -25  -90  91

# TARGET: human hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CTGDIR=/hive/data/genomes/hg38/hg38.contigs.2bit
SEQ1_CTGLEN=/hive/data/genomes/hg38/hg38.contigs.chrom.sizes
SEQ1_LIFT=/hive/data/genomes/hg38/jkStuff/hg38.contigs.lift
SEQ1_CHUNK=40000000
SEQ1_LIMIT=30
SEQ1_LAP=10000

# QUERY: X. tropicalis xenTro7
SEQ2_DIR=/hive/data/genomes/xenTro7/xenTro7.2bit
SEQ2_LEN=/hive/data/genomes/xenTro7/chrom.sizes
SEQ2_CHUNK=20000000
SEQ2_LIMIT=20
SEQ2_LAP=0

BASE=/hive/data/genomes/hg38/bed/lastzXenTro7.2015-02-18
TMPDIR=/dev/shm
'_EOF_'
    # << happy emacs

    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
        -chainMinScore=5000 -chainLinearGap=loose \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > do.log 2>&1
    # real    1991m40.229s

    cat fb.hg38.chainXenTro7Link.txt
    # 116213822 bases of 3049335806 (3.811%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` hg38 xenTro7) \
       > rbest.log 2>&1 &
    # real    15m54.917s

    # and for the swap:
    mkdir /hive/data/genomes/xenTro7/bed/blastz.hg38.swap
    cd /hive/data/genomes/xenTro7/bed/blastz.hg38.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/hg38/bed/lastzXenTro7.2015-02-18/DEF \
        -swap -chainMinScore=5000 -chainLinearGap=loose \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    #  real    53m28.988s

    cat fb.xenTro7.chainHg38Link.txt
    # 108823737 bases of 1365936747 (7.967%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` xenTro7 hg38) \
       > rbest.log 2>&1
    # real    16m4.622s

#########################################################################
# LASTZ human/hg38 vs. Coelacanth/latCha1 - (DONE - 2015-02-18 - Hiram)
    mkdir /hive/data/genomes/hg38/bed/lastzLatCha1.2015-02-18
    cd /hive/data/genomes/hg38/bed/lastzLatCha1.2015-02-18

    cat << '_EOF_' > DEF
# human vs Coelacanth
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.54/bin/lastz
BLASTZ_O=400
BLASTZ_E=30
BLASTZ_Y=3400
BLASTZ_L=6000
BLASTZ_K=2200
BLASTZ_M=50
BLASTZ_Q=/scratch/data/blastz/HoxD55.q
#      A    C    G    T
#     91  -90  -25 -100
#    -90  100 -100  -25
#    -25 -100  100  -90
#   -100  -25  -90  91

# TARGET: human hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CTGDIR=/hive/data/genomes/hg38/hg38.contigs.2bit
SEQ1_CTGLEN=/hive/data/genomes/hg38/hg38.contigs.chrom.sizes
SEQ1_LIFT=/hive/data/genomes/hg38/jkStuff/hg38.contigs.lift
SEQ1_CHUNK=40000000
SEQ1_LIMIT=30
SEQ1_LAP=10000

# QUERY: Coelacanth latCha1
SEQ2_DIR=/hive/data/genomes/latCha1/latCha1.2bit
SEQ2_LEN=/hive/data/genomes/latCha1/chrom.sizes
SEQ2_CHUNK=20000000
SEQ2_LIMIT=20
SEQ2_LAP=0

BASE=/hive/data/genomes/hg38/bed/lastzLatCha1.2015-02-18
TMPDIR=/dev/shm
'_EOF_'
    # << happy emacs

    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
        -chainMinScore=5000 -chainLinearGap=loose \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > do.log 2>&1
    # real    2036m36.030s

    cat fb.hg38.chainLatCha1Link.txt
    # 87594238 bases of 3049335806 (2.873%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` hg38 latCha1) \
       > rbest.log 2>&1 &
    # real    8m36.393s

    # and for the swap:
    mkdir /hive/data/genomes/latCha1/bed/blastz.hg38.swap
    cd /hive/data/genomes/latCha1/bed/blastz.hg38.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/hg38/bed/lastzLatCha1.2015-02-18/DEF \
        -swap -chainMinScore=5000 -chainLinearGap=loose \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    #  real    19m14.665s

    cat fb.latCha1.chainHg38Link.txt
    # 75312106 bases of 2183592768 (3.449%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` latCha1 hg38) \
       > rbest.log 2>&1
    # real    10m14.893s

#########################################################################
# LASTZ human/hg38 vs. Spotted gar/lepOcu1 - (DONE - 2015-02-18 - Hiram)
    mkdir /hive/data/genomes/hg38/bed/lastzLepOcu1.2015-02-18
    cd /hive/data/genomes/hg38/bed/lastzLepOcu1.2015-02-18

    cat << '_EOF_' > DEF
# human vs Spotted gar
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.54/bin/lastz
BLASTZ_O=400
BLASTZ_E=30
BLASTZ_Y=3400
BLASTZ_L=6000
BLASTZ_K=2200
BLASTZ_M=50
BLASTZ_Q=/scratch/data/blastz/HoxD55.q
#      A    C    G    T
#     91  -90  -25 -100
#    -90  100 -100  -25
#    -25 -100  100  -90
#   -100  -25  -90  91

# TARGET: human hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CTGDIR=/hive/data/genomes/hg38/hg38.contigs.2bit
SEQ1_CTGLEN=/hive/data/genomes/hg38/hg38.contigs.chrom.sizes
SEQ1_LIFT=/hive/data/genomes/hg38/jkStuff/hg38.contigs.lift
SEQ1_CHUNK=40000000
SEQ1_LIMIT=30
SEQ1_LAP=10000

# QUERY: Spotted gar lepOcu1
SEQ2_DIR=/hive/data/genomes/lepOcu1/lepOcu1.2bit
SEQ2_LEN=/hive/data/genomes/lepOcu1/chrom.sizes
SEQ2_CHUNK=20000000
SEQ2_LIMIT=20
SEQ2_LAP=0

BASE=/hive/data/genomes/hg38/bed/lastzLepOcu1.2015-02-18
TMPDIR=/dev/shm
'_EOF_'
    # << happy emacs

    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
        -chainMinScore=5000 -chainLinearGap=loose \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > do.log 2>&1
    # real    917m10.105s

    cat fb.hg38.chainLepOcu1Link.txt
    # 76570858 bases of 3049335806 (2.511%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` hg38 lepOcu1) \
       > rbest.log 2>&1 &
    # real    11m4.401s

    # and for the swap:
    mkdir /hive/data/genomes/lepOcu1/bed/blastz.hg38.swap
    cd /hive/data/genomes/lepOcu1/bed/blastz.hg38.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/hg38/bed/lastzLepOcu1.2015-02-18/DEF \
        -swap -chainMinScore=5000 -chainLinearGap=loose \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    #  real    8m52.863s

    cat fb.lepOcu1.chainHg38Link.txt
    # 57676637 bases of 869414361 (6.634%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` lepOcu1 hg38) \
       > rbest.log 2>&1
    # real    8m31.395s

#########################################################################
# LASTZ human/hg38 Tree shrew/tupBel1 - (DONE - 2015-03-27 - Hiram)
#   re-running with default parameters, this provides more coverage
    mkdir /hive/data/genomes/hg38/bed/lastzTupBel1.2015-03-27
    cd /hive/data/genomes/hg38/bed/lastzTupBel1.2015-03-27

    cat << '_EOF_' > DEF
# human vs Tree shrew
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.54/bin/lastz
BLASTZ_M=254

# TARGET: human hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CTGDIR=/hive/data/genomes/hg38/hg38.contigs.2bit
SEQ1_CTGLEN=/hive/data/genomes/hg38/hg38.contigs.chrom.sizes
SEQ1_LIFT=/hive/data/genomes/hg38/jkStuff/hg38.contigs.lift
SEQ1_CHUNK=40000000
SEQ1_LIMIT=10
SEQ1_LAP=10000

# QUERY: Tree shrew tupBel1
SEQ2_DIR=/hive/data/genomes/tupBel1/tupBel1.2bit
SEQ2_LEN=/hive/data/genomes/tupBel1/chrom.sizes
SEQ2_CHUNK=20000000
SEQ2_LIMIT=300
SEQ2_LAP=0

BASE=/hive/data/genomes/hg38/bed/lastzTupBel1.2015-03-27
TMPDIR=/dev/shm
'_EOF_'
    # << happy emacs

    time (doBlastzChainNet.pl -verbose=2 `pwd`/DEF \
  -chainMinScore=3000 -chainLinearGap=medium \
     -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku) > do.log 2>&1
    # real    372m50.142s

    cat fb.hg38.chainTupBel1Link.txt
    # 1067849727 bases of 3049335806 (35.019%) in intersection
    # replacing the previous tuned version:
    # 753229970 bases of 3049335806 (24.701%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` hg38 tupBel1) > rbest.log 2>&1 &
    # real    33m33.647s

    # and for the swap:
    mkdir /hive/data/genomes/tupBel1/bed/blastz.hg38.swap
    cd /hive/data/genomes/tupBel1/bed/blastz.hg38.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/hg38/bed/lastzTupBel1.2015-03-27/DEF \
        -swap -chainMinScore=3000 -chainLinearGap=medium \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    #  real    256m18.000s

    cat fb.tupBel1.chainHg38Link.txt
    # 1056254191 bases of 2137225476 (49.422%) in intersection
    # replacing the previous tuned version:
    # 749930137 bases of 2137225476 (35.089%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` tupBel1 hg38) > rbest.log 2>&1
    # real    112m44.439s

#########################################################################
# LASTZ human/hg38 Tree mouse/mm10 - (DONE - 2015-04-10 - Hiram)
#   re-running to correct missing contig alignments from canFam3
    mkdir /hive/data/genomes/hg38/bed/lastzMm10.2015-04-08
    cd /hive/data/genomes/hg38/bed/lastzMm10.2015-04-08

    cat << '_EOF_' > DEF
# human vs mouse
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz

# TARGET: Human Hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CTGDIR=/hive/data/genomes/hg38/hg38.contigs.2bit
SEQ1_CTGLEN=/hive/data/genomes/hg38/hg38.contigs.chrom.sizes
SEQ1_LIFT=/hive/data/genomes/hg38/jkStuff/hg38.contigs.lift
SEQ1_CHUNK=40000000
SEQ1_LAP=10000

# QUERY: Mouse Mm10
SEQ2_DIR=/scratch/data/mm10/mm10.2bit
SEQ2_LEN=/scratch/data/mm10/chrom.sizes
SEQ2_CHUNK=20000000
SEQ2_LAP=0

BASE=/hive/data/genomes/hg38/bed/lastzMm10.2015-04-08
TMPDIR=/dev/shm
'_EOF_'
    # << happy emacs

    time (doBlastzChainNet.pl -verbose=2 `pwd`/DEF \
        -syntenicNet -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
        -fileServer=hgwdev -chainMinScore=3000 -chainLinearGap=medium) \
           > do.log 2>&1
    # real    323m51.165s

    cat fb.hg38.chainMm10Link.txt
    # 965211935 bases of 3049335806 (31.653%) in intersection
    # replacing the broken run from Jan 2014:
    # 964465044 bases of 3049335806 (31.629%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` hg38 mm10) > rbest.log 2>&1 &
    # real    32m22.990s

    # load up the recip best chainNet tables
    time (doRecipBest.pl -load -continue=load -workhorse=hgwdev \
	-buildDir=`pwd` hg38 mm10) > loadRBest.log 2>&1 &
    cat fb.hg38.chainRBestMm10Link.txt
# 891562094 bases of 3049335806 (29.238%) in intersection

    # create and load up the syntenic chainNet tables 2017-10-30
cd /hive/data/genomes/hg38/bed/lastzMm10.2015-04-08/axtChain
netToAxt hg38.mm10.syn.net.gz hg38.mm10.all.chain.gz \
/scratch/data/hg38/hg38.2bit /hive/data/genomes/mm10/mm10.2bit stdout \
  | axtSort stdin stdout \
     | axtToChain stdin /hive/data/genomes/hg38/chrom.sizes \
        /hive/data/genomes/mm10/chrom.sizes stdout \
            | gzip -c > hg38.mm10.syn.chain.gz
hgLoadChain -tIndex hg38 chainSynMm10 hg38.mm10.syn.chain.gz
netFilter -minGap=10 hg38.mm10.syn.net.gz \
  | hgLoadNet -verbose=0 hg38 netSynMm10 stdin
cd /hive/data/genomes/hg38/bed/lastzMm10.2015-04-08
featureBits hg38 chainSynMm10Link > fb.hg38.chainSynMm10Link.txt 2>&1
cat fb.hg38.chainSynMm10Link.txt
# 913707143 bases of 3049335806 (29.964%) in intersection

    # and for the swap:
    mkdir /hive/data/genomes/mm10/bed/blastz.hg38.swap
    cd /hive/data/genomes/mm10/bed/blastz.hg38.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/hg38/bed/lastzMm10.2015-04-08/DEF \
        -swap -chainMinScore=3000 -chainLinearGap=medium \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    #  real    74m49.827s

    cat fb.mm10.chainHg38Link.txt
    # 938348519 bases of 2652783500 (35.372%) in intersection
    # replacing the broken run from Jan 2014:
    # 937030766 bases of 2652783500 (35.323%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` mm10 hg38) > rbest.log 2>&1
    # real    32m38.549s

#########################################################################
# LASTZ human/hg38 Tree dog/canFam3 - (DONE - 2015-04-10 - Hiram)
#   re-running to correct missing contig alignments from canFam3
    mkdir /hive/data/genomes/hg38/bed/lastzCanFam3.2015-04-08
    cd /hive/data/genomes/hg38/bed/lastzCanFam3.2015-04-08

    cat << '_EOF_' > DEF
# human vs dog
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz

# TARGET: Human Hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CTGDIR=/hive/data/genomes/hg38/hg38.contigs.2bit
SEQ1_CTGLEN=/hive/data/genomes/hg38/hg38.contigs.chrom.sizes
SEQ1_LIFT=/hive/data/genomes/hg38/jkStuff/hg38.contigs.lift
SEQ1_CHUNK=20000000
SEQ1_LAP=10000

# QUERY: Dog CanFam3
SEQ2_DIR=/hive/data/genomes/canFam3/canFam3.2bit
SEQ2_LEN=/hive/data/genomes/canFam3/chrom.sizes
SEQ2_CHUNK=20000000
SEQ2_LAP=0

BASE=/hive/data/genomes/hg38/bed/lastzCanFam3.2015-04-08
TMPDIR=/dev/shm
'_EOF_'
    # << happy emacs

    time (doBlastzChainNet.pl -verbose=2 `pwd`/DEF \
        -syntenicNet -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
        -fileServer=hgwdev -chainMinScore=3000 -chainLinearGap=medium) \
          > do.log 2>&1
    # real    821m15.144s

    cat fb.hg38.chainCanFam3Link.txt
    # 1536721546 bases of 3049335806 (50.395%) in intersection
    # replacing the broken one from Jan 2014:
    # 1523987456 bases of 3049335806 (49.978%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` hg38 canFam3) > rbest.log 2>&1 &
    # real    42m21.276s

    # load up the recip best chainNet tables
    time (doRecipBest.pl -load -continue=load -workhorse=hgwdev \
	-buildDir=`pwd` hg38 canFam3) > loadRBest.log 2>&1 &
    cat fb.hg38.chainRBestCanFam3Link.txt
# 1415877801 bases of 3049335806 (46.432%) in intersection

    # create and load up the syntenic chainNet tables 2017-10-30
cd /hive/data/genomes/hg38/bed/lastzCanFam3.2015-04-08/axtChain
netToAxt hg38.canFam3.syn.net.gz hg38.canFam3.all.chain.gz \
/scratch/data/hg38/hg38.2bit /hive/data/genomes/canFam3/canFam3.2bit stdout \
  | axtSort stdin stdout \
     | axtToChain stdin /hive/data/genomes/hg38/chrom.sizes \
        /hive/data/genomes/canFam3/chrom.sizes stdout \
            | gzip -c > hg38.canFam3.syn.chain.gz
hgLoadChain -tIndex hg38 chainSynCanFam3 hg38.canFam3.syn.chain.gz
netFilter -minGap=10 hg38.canFam3.syn.net.gz \
  | hgLoadNet -verbose=0 hg38 netSynCanFam3 stdin
cd /hive/data/genomes/hg38/bed/lastzCanFam3.2015-04-08
featureBits hg38 chainSynCanFam3Link > fb.hg38.chainSynCanFam3Link.txt 2>&1
cat fb.hg38.chainSynCanFam3Link.txt
# 1478843439 bases of 3049335806 (48.497%) in intersection

    # and for the swap:
    mkdir /hive/data/genomes/canFam3/bed/blastz.hg38.swap
    cd /hive/data/genomes/canFam3/bed/blastz.hg38.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/hg38/bed/lastzCanFam3.2015-04-08/DEF \
        -swap -chainMinScore=3000 -chainLinearGap=medium \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    #  real    105m19.994s

    cat fb.canFam3.chainHg38Link.txt
    # 1456224911 bases of 2392715236 (60.861%) in intersection
    # replacing the broken one from Jan 2014:
    # 1437624815 bases of 2392715236 (60.083%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` canFam3 hg38) > rbest.log 2>&1
    # real    43m54.042s

#########################################################################
# LASTZ human/hg38 Tree dog/rheMac3 - (DONE - 2015-04-10 - Hiram)
#   re-running to correct missing contig alignments from rheMac3
    mkdir /hive/data/genomes/hg38/bed/lastzRheMac3.2015-04-08
    cd /hive/data/genomes/hg38/bed/lastzRheMac3.2015-04-08

    cat << '_EOF_' > DEF
# human vs macaca mulatta
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz
# maximum M allowed with lastz is only 254
BLASTZ_M=254
BLASTZ_Q=/scratch/data/blastz/human_chimp.v2.q
BLASTZ_O=600
BLASTZ_E=150
# other parameters from panTro2 vs hg18 lastz on advice from Webb
BLASTZ_K=4500
BLASTZ_Y=15000
BLASTZ_T=2

# TARGET: Human Hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CTGDIR=/hive/data/genomes/hg38/hg38.contigs.2bit
SEQ1_CTGLEN=/hive/data/genomes/hg38/hg38.contigs.chrom.sizes
SEQ1_LIFT=/hive/data/genomes/hg38/jkStuff/hg38.contigs.lift
SEQ1_CHUNK=20000000
SEQ1_LAP=10000

# QUERY: Macaca Mulatta RheMac3
SEQ2_DIR=/scratch/data/rheMac3/rheMac3.2bit
SEQ2_LEN=/scratch/data/rheMac3/chrom.sizes
SEQ2_CHUNK=20000000
SEQ2_LAP=0
SEQ2_IN_CONTIGS=0

BASE=/hive/data/genomes/hg38/bed/lastzRheMac3.2015-04-08
TMPDIR=/dev/shm
'_EOF_'
    # << happy emacs

    time (doBlastzChainNet.pl -verbose=2 `pwd`/DEF \
        -syntenicNet -fileServer=hgwdev \
        -chainMinScore=5000 -chainLinearGap=medium \
        -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku) \
          > do.log 2>&1
    # real    193m23.828s

    cat fb.hg38.chainRheMac3Link.txt
    # 2464716257 bases of 3049335806 (80.828%) in intersection
    # replacing the broken one from Jan 2014:
    # 2431208700 bases of 3049335806 (79.729%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` hg38 rheMac3) > rbest.log 2>&1 &
    # real    38m25.112s

    # and for the swap:
    mkdir /hive/data/genomes/rheMac3/bed/blastz.hg38.swap
    cd /hive/data/genomes/rheMac3/bed/blastz.hg38.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/hg38/bed/lastzRheMac3.2015-04-08/DEF \
        -swap -chainMinScore=5000 -chainLinearGap=medium \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    #  real    83m14.955s

    cat fb.rheMac3.chainHg38Link.txt
    # 2328257435 bases of 2639145830 (88.220%) in intersection
    # replacing the broken one from Jan 2014:
    # 2288533769 bases of 2639145830 (86.715%) in intersection


    time (doRecipBest.pl -buildDir=`pwd` rheMac3 hg38) > rbest.log 2>&1
    # real    39m52.256s

#########################################################################
# LASTZ human/hg38 Tree mouse/mm10 - (DONE - 2015-04-30 - Hiram)
#   experiment to see if lineage specific repeats does more coverage
    mkdir /hive/data/genomes/hg38/bed/lastzMm10.2015-04-30
    cd /hive/data/genomes/hg38/bed/lastzMm10.2015-04-30

    cat << '_EOF_' > DEF
# human vs mouse
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz
BLASTZ_ABRIDGE_REPEATS=1

# TARGET: Human Hg38
SEQ1_DIR=/scratch/data/hg38/nib
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_SMSK=/hive/data/genomes/hg38/bed/linSpecRep/humanSpecific
SEQ1_CHUNK=40000000
SEQ1_LAP=10000

# QUERY: Mouse Mm10
SEQ2_DIR=/scratch/data/mm10/nib
SEQ2_SMSK=/scratch/data/mm10/notInOthers
SEQ2_LEN=/scratch/data/mm10/chrom.sizes
SEQ2_CHUNK=20000000
SEQ2_LAP=0

BASE=/hive/data/genomes/hg38/bed/lastzMm10.2015-04-30
TMPDIR=/dev/shm
'_EOF_'
    # << happy emacs

    time (doBlastzChainNet.pl -stop=net -verbose=2 `pwd`/DEF \
        -syntenicNet -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
        -fileServer=hgwdev -chainMinScore=3000 -chainLinearGap=medium) \
           > net.log 2>&1
    # real    323m51.165s
    # test load, -debug to generate loadUp.csh, then modify the table names
    doBlastzChainNet.pl -stop=net -verbose=2 `pwd`/DEF -continue=load -debug \
      -syntenicNet -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
      -stop=load -fileServer=hgwdev -chainMinScore=3000 -chainLinearGap=medium
           > net.log 2>&1
    # real    167m38.082s

    cat fb.hg38.chainMm10Link.txt
    #  1044599372 bases of 3049335806 (34.257%) in intersection
    # this procedure does produce more coverage

    cat fb.hg38.chainMm10Link.txt
    # 965211935 bases of 3049335806 (31.653%) in intersection
    # replacing the broken run from Jan 2014:
    # 964465044 bases of 3049335806 (31.629%) in intersection

    # XXX experiment concluded, not continued from here
    time (doRecipBest.pl -buildDir=`pwd` hg38 mm10) > rbest.log 2>&1 &
    # real    32m22.990s

    # and for the swap:
    mkdir /hive/data/genomes/mm10/bed/blastz.hg38.swap
    cd /hive/data/genomes/mm10/bed/blastz.hg38.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/hg38/bed/lastzMm10.2015-04-30/DEF \
        -swap -chainMinScore=3000 -chainLinearGap=medium \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    #  real    74m49.827s

    cat fb.mm10.chainHg38Link.txt
    # 938348519 bases of 2652783500 (35.372%) in intersection
    # replacing the broken run from Jan 2014:
    # 937030766 bases of 2652783500 (35.323%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` mm10 hg38) > rbest.log 2>&1
    # real    32m38.549s

#########################################################################
# LASTZ human/hg38 Mouse lemur/micMur2 - (DONE - 2015-05-05 - Hiram)
    # for some odd reason, these results were lost
    # the same procedure was re-run March 2015 in: lastzMicMur2.2015-03-17
    mkdir /hive/data/genomes/hg38/bed/lastzMicMur2.2015-05-06
    cd /hive/data/genomes/hg38/bed/lastzMicMur2.2015-05-06

    cp -p \
/hive/users/hiram/multiz/100way/hg38.micMur2/hg38.micMur2.tuning.top400.txt \
     ./hg38.micMur2.tuning.Q.txt

    cat << '_EOF_' > DEF
# human vs Mouse lemur
# parameters obtained from a tuning run of lastz_D
#  /hive/users/hiram/multiz/100way/hg38.micMur2/hg38.micMur2.tuning.top400.txt
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz
BLASTZ_T=2
BLASTZ_O=400
BLASTZ_E=30
BLASTZ_M=254
BLASTZ_X=1000
BLASTZ_Y=3400
BLASTZ_Q=/hive/data/genomes/hg38/bed/lastzMicMur2.2015-05-06/hg38.micMur2.tuning.Q.txt
#       A     C     G     T
# A   100  -164   -34  -127
# C  -164    93  -186   -34
# G   -34  -186    93  -164
# T  -127   -34  -164   100

# TARGET: human hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CTGDIR=/hive/data/genomes/hg38/hg38.contigs.2bit
SEQ1_CTGLEN=/hive/data/genomes/hg38/hg38.contigs.chrom.sizes
SEQ1_LIFT=/hive/data/genomes/hg38/jkStuff/hg38.contigs.lift
SEQ1_CHUNK=40000000
SEQ1_LIMIT=10
SEQ1_LAP=10000

# QUERY: Mouse lemur micMur2
SEQ2_DIR=/hive/data/genomes/micMur2/micMur2.2bit
SEQ2_LEN=/hive/data/genomes/micMur2/chrom.sizes
SEQ2_CHUNK=20000000
SEQ2_LIMIT=20
SEQ2_LAP=0

BASE=/hive/data/genomes/hg38/bed/lastzMicMur2.2015-05-06
TMPDIR=/dev/shm
'_EOF_'
    # << happy emacs

    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
        -chainMinScore=3000 -chainLinearGap=medium \
          -workhorse=hgwdev -smallClusterHub=ku \
            -bigClusterHub=ku -syntenicNet) > do.log 2>&1
    # real    286m0.829s

    cat fb.hg38.chainMicMur2Link.txt
    # 1632306331 bases of 3049335806 (53.530%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` hg38 micMur2) > rbest.log 2>&1 &
    # real    37m38.749s

    # and for the swap:
    mkdir /hive/data/genomes/micMur2/bed/blastz.hg38.swap
    cd /hive/data/genomes/micMur2/bed/blastz.hg38.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/hg38/bed/lastzMicMur2.2015-05-06/DEF \
        -swap -chainMinScore=3000 -chainLinearGap=medium \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    #  real    108m50.264s

    cat fb.micMur2.chainHg38Link.txt
    # 1587083892 bases of 2377775715 (66.747%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` micMur2 hg38) \
      > rbest.log 2>&1
    # real    59m8.207s

#########################################################################
# LASTZ human/hg38 Tree chimp/rheMac8 - (DONE - 2016-02-05 - Hiram)
    mkdir /hive/data/genomes/hg38/bed/lastzRheMac8.2016-02-05
    cd /hive/data/genomes/hg38/bed/lastzRheMac8.2016-02-05

    printf '# human vs macaca mulatta
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz
# maximum M allowed with lastz is only 254
BLASTZ_M=254
BLASTZ_Q=/scratch/data/blastz/human_chimp.v2.q
BLASTZ_O=600
BLASTZ_E=150
# other parameters from panTro2 vs hg18 lastz on advice from Webb
BLASTZ_K=4500
BLASTZ_Y=15000
BLASTZ_T=2

# TARGET: Human Hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CTGDIR=/hive/data/genomes/hg38/hg38.contigs.2bit
SEQ1_CTGLEN=/hive/data/genomes/hg38/hg38.contigs.chrom.sizes
SEQ1_LIFT=/hive/data/genomes/hg38/jkStuff/hg38.contigs.lift
SEQ1_CHUNK=20000000
SEQ1_LAP=10000

# QUERY: Macaca Mulatta RheMac8
SEQ2_DIR=/hive/data/genomes/rheMac8/rheMac8.2bit
SEQ2_LEN=/hive/data/genomes/rheMac8/chrom.sizes
SEQ2_CHUNK=20000000
SEQ2_LIMIT=600
SEQ2_LAP=0
SEQ2_IN_CONTIGS=0

BASE=/hive/data/genomes/hg38/bed/lastzRheMac8.2016-02-05
TMPDIR=/dev/shm
' > DEF
    # << happy emacs

    time (doBlastzChainNet.pl -verbose=2 `pwd`/DEF \
        -syntenicNet -fileServer=hgwdev \
        -chainMinScore=5000 -chainLinearGap=medium \
        -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku) > do.log 2>&1
    # real    4099m2.582s

    # broken cluster run, continuing:
    time (doBlastzChainNet.pl -verbose=2 `pwd`/DEF \
        -continue=cat -syntenicNet -fileServer=hgwdev \
        -chainMinScore=5000 -chainLinearGap=medium \
        -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku) > cat.log 2>&1
    #  real    101m51.644s


    cat fb.hg38.chainRheMac8Link.txt
    # 2576861166 bases of 3049335806 (84.506%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` hg38 rheMac8) > rbest.log 2>&1 &
    # real    182m11.216s
    time (doRecipBest.pl -load -continue=load -workhorse=hgwdev \
	-buildDir=`pwd` hg38 rheMac8) > loadRBest.log 2>&1 &
    cat fb.hg38.chainRBestRheMac8Link.txt
    # 2401566032 bases of 3049335806 (78.757%) in intersection

    # create and load up syntenic chainNet: 2017-10-27
cd /hive/data/genomes/hg38/bed/lastzRheMac8.2016-02-05/axtChain
netToAxt hg38.rheMac8.syn.net.gz hg38.rheMac8.all.chain.gz \
/scratch/data/hg38/hg38.2bit /hive/data/genomes/rheMac8/rheMac8.2bit stdout \
  | axtSort stdin stdout \
     | axtToChain stdin /hive/data/genomes/hg38/chrom.sizes \
        /hive/data/genomes/rheMac8/chrom.sizes stdout \
            | gzip -c > hg38.rheMac8.syn.chain.gz
hgLoadChain -tIndex hg38 chainSynRheMac8 hg38.rheMac8.syn.chain.gz
netFilter -minGap=10 hg38.rheMac8.syn.net.gz \
  | hgLoadNet -verbose=0 hg38 netSynRheMac8 stdin
cd /hive/data/genomes/hg38/bed/lastzRheMac8.2016-02-05
featureBits hg38 chainSynRheMac8Link > fb.hg38.chainSynRheMac8Link.txt 2>&1
cat fb.hg38.chainSynRheMac8Link.txt
# 2535752862 bases of 3049335806 (83.158%) in intersection

    # and for the swap:
    mkdir /hive/data/genomes/rheMac8/bed/blastz.hg38.swap
    cd /hive/data/genomes/rheMac8/bed/blastz.hg38.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/hg38/bed/lastzRheMac8.2016-02-05/DEF \
        -swap -chainMinScore=5000 -chainLinearGap=medium \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    #  real    234m24.287s

    cat fb.rheMac8.chainHg38Link.txt
    # 2499211352 bases of 3142093174 (79.540%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` rheMac8 hg38) > rbest.log 2>&1
    # real    355m16.431s

#########################################################################
# LASTZ human/hg38 vs. chicken/galGal5 - (DONE - 2016-04-19 - Hiram)
    mkdir /hive/data/genomes/hg38/bed/lastzGalGal5.2016-04-19
    cd /hive/data/genomes/hg38/bed/lastzGalGal5.2016-04-19

    printf "# human vs chicken
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.54/bin/lastz
BLASTZ_O=400
BLASTZ_E=30
BLASTZ_Y=3400
BLASTZ_L=6000
BLASTZ_K=2200
BLASTZ_M=50
BLASTZ_Q=/scratch/data/blastz/HoxD55.q
#      A    C    G    T
#     91  -90  -25 -100
#    -90  100 -100  -25
#    -25 -100  100  -90
#   -100  -25  -90  91

# TARGET: human hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CTGDIR=/hive/data/genomes/hg38/hg38.contigs.2bit
SEQ1_CTGLEN=/hive/data/genomes/hg38/hg38.contigs.chrom.sizes
SEQ1_LIFT=/hive/data/genomes/hg38/jkStuff/hg38.contigs.lift
SEQ1_CHUNK=40000000
SEQ1_LIMIT=30
SEQ1_LAP=10000

# QUERY: chicken galGal5
SEQ2_DIR=/hive/data/genomes/galGal5/galGal5.2bit
SEQ2_LEN=/hive/data/genomes/galGal5/chrom.sizes
SEQ2_CHUNK=20000000
SEQ2_LIMIT=30
SEQ2_LAP=0

BASE=/hive/data/genomes/hg38/bed/lastzGalGal5.2016-04-19
TMPDIR=/dev/shm
" > DEF
    # << happy emacs

    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
        -chainMinScore=5000 -chainLinearGap=loose \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > do.log 2>&1
    # real    341m2.910s

    cat fb.hg38.chainGalGal5Link.txt
    # 155942333 bases of 3049335806 (5.114%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` hg38 galGal5) > rbest.log 2>&1 &
    # real    235m31.028s

    # and for the swap:
    mkdir /hive/data/genomes/galGal5/bed/blastz.hg38.swap
    cd /hive/data/genomes/galGal5/bed/blastz.hg38.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/hg38/bed/lastzGalGal5.2016-04-19/DEF \
        -swap -chainMinScore=5000 -chainLinearGap=loose \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    #  real    17m45.055s

    cat fb.galGal5.chainHg38Link.txt
    # 131657596 bases of 1218501075 (10.805%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` galGal5 hg38) > rbest.log 2>&1
    # real    196m46.991s

#########################################################################
# LASTZ human/hg38 vs. Malayan flying lemur/galVar1 - (DONE - 2016-04-25 - Hiram)
    mkdir /hive/data/genomes/hg38/bed/lastzGalVar1.2016-04-25
    cd /hive/data/genomes/hg38/bed/lastzGalVar1.2016-04-25

    printf "# human vs Malayan flying lemur
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz
BLASTZ_O=400
BLASTZ_E=30
BLASTZ_M=254
# default BLASTZ_Q score matrix:
#       A     C     G     T
# A    91  -114   -31  -123
# C  -114   100  -125   -31
# G   -31  -125   100  -114
# T  -123   -31  -114    91

# TARGET: human hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CTGDIR=/hive/data/genomes/hg38/hg38.contigs.2bit
SEQ1_CTGLEN=/hive/data/genomes/hg38/hg38.contigs.chrom.sizes
SEQ1_LIFT=/hive/data/genomes/hg38/jkStuff/hg38.contigs.lift
SEQ1_CHUNK=40000000
SEQ1_LIMIT=30
SEQ1_LAP=10000

# QUERY: Malayan flying lemur galVar1
SEQ2_DIR=/hive/data/genomes/galVar1/galVar1.2bit
SEQ2_LEN=/hive/data/genomes/galVar1/chrom.sizes
SEQ2_CHUNK=20000000
SEQ2_LIMIT=400
SEQ2_LAP=0

BASE=/hive/data/genomes/hg38/bed/lastzGalVar1.2016-04-25
TMPDIR=/dev/shm
" > DEF
    # << happy emacs

    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
        -chainMinScore=3000 -chainLinearGap=medium \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > do.log 2>&1
    # real    916m34.893s

    cat fb.hg38.chainGalVar1Link.txt
    # 1739210426 bases of 3049335806 (57.036%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` hg38 galVar1) \
       > rbest.log 2>&1 &
    # real    1055m58.835s

    # and for the swap:
    mkdir /hive/data/genomes/galVar1/bed/blastz.hg38.swap
    cd /hive/data/genomes/galVar1/bed/blastz.hg38.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/hg38/bed/lastzGalVar1.2016-04-25/DEF \
        -swap -chainMinScore=3000 -chainLinearGap=medium \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    #  real    357m45.647s

    cat fb.galVar1.chainHg38Link.txt
    # 1818567752 bases of 2802917674 (64.881%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` galVar1 hg38) \
        > rbest.log 2>&1
    # real    1774m42.560s

#########################################################################
# LASTZ human/hg38 Gorilla/panPan2 - (DONE - 2016-05-24 - Hiram)
    mkdir /hive/data/genomes/hg38/bed/lastzPanPan2.2016-05-24
    cd /hive/data/genomes/hg38/bed/lastzPanPan2.2016-05-24

    cp -p \
/hive/users/hiram/multiz/100way/hg38.panPan2/hg38.panPan2.tuning.top200.txt \
     ./hg38.panPan2.tuning.Q.txt

    printf '# human vs bonobo
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz
BLASTZ_T=2
BLASTZ_O=600
BLASTZ_E=150
BLASTZ_M=254
BLASTZ_K=4500
BLASTZ_L=4500
BLASTZ_Y=15000
BLASTZ_Q=/scratch/data/blastz/human_chimp.v2.q
#       A     C     G     T
# A    90  -330  -236  -356
# C  -330   100  -318  -236
# G  -236  -318   100  -330
# T  -356  -236  -330    90

# TARGET: human hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CTGDIR=/hive/data/genomes/hg38/hg38.contigs.2bit
SEQ1_CTGLEN=/hive/data/genomes/hg38/hg38.contigs.chrom.sizes
SEQ1_LIFT=/hive/data/genomes/hg38/jkStuff/hg38.contigs.lift
SEQ1_CHUNK=40000000
SEQ1_LIMIT=10
SEQ1_LAP=10000

# QUERY: bonobo panPan2
SEQ2_DIR=/hive/data/genomes/panPan2/panPan2.2bit
SEQ2_LEN=/hive/data/genomes/panPan2/chrom.sizes
SEQ2_CHUNK=20000000
SEQ2_LIMIT=50
SEQ2_LAP=0

BASE=/hive/data/genomes/hg38/bed/lastzPanPan2.2016-05-24
TMPDIR=/dev/shm
' > DEF

    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
        -chainMinScore=3000 -chainLinearGap=medium \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > do.log 2>&1
    # real    203m58.095s

    cat fb.hg38.chainPanPan2Link.txt
    # 2826289232 bases of 3049335806 (92.685%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` hg38 panPan2) \
      > rbest.log 2>&1 &
    # real    184m43.685s
    time (doRecipBest.pl -load -continue=load -workhorse=hgwdev \
	-buildDir=`pwd` hg38 panPan2) > loadRBest.log 2>&1 &
    cat fb.hg38.chainRBestPanPan2Link.txt
    # 2653262611 bases of 3049335806 (87.011%) in intersection

    # create and load up syntenic chainNet: 2017-10-27
cd /hive/data/genomes/hg38/bed/lastzPanPan2.2016-05-24/axtChain
netToAxt hg38.panPan2.syn.net.gz hg38.panPan2.all.chain.gz \
/scratch/data/hg38/hg38.2bit /hive/data/genomes/panPan2/panPan2.2bit stdout \
  | axtSort stdin stdout \
     | axtToChain stdin /hive/data/genomes/hg38/chrom.sizes \
        /hive/data/genomes/panPan2/chrom.sizes stdout \
            | gzip -c > hg38.panPan2.syn.chain.gz
hgLoadChain -tIndex hg38 chainSynPanPan2 hg38.panPan2.syn.chain.gz
netFilter -minGap=10 hg38.panPan2.syn.net.gz \
  | hgLoadNet -verbose=0 hg38 netSynPanPan2 stdin
cd /hive/data/genomes/hg38/bed/lastzPanPan2.2016-05-24
featureBits hg38 chainSynPanPan2Link > fb.hg38.chainSynPanPan2Link.txt 2>&1
cat fb.hg38.chainSynPanPan2Link.txt
# 2790018893 bases of 3049335806 (91.496%) in intersection

    # and for the swap:
    mkdir /hive/data/genomes/panPan2/bed/blastz.hg38.swap
    cd /hive/data/genomes/panPan2/bed/blastz.hg38.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/hg38/bed/lastzPanPan2.2016-05-24/DEF \
        -swap -chainMinScore=3000 -chainLinearGap=medium \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    #  real    127m16.000s

    cat fb.panPan2.chainHg38Link.txt
    # 2664377492 bases of 2725937399 (97.742%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` panPan2 hg38) > rbest.log 2>&1
    # real    84m33.540s

#########################################################################
# LASTZ human/hg38 vs. Killer whale/orcOrc1 - (DONE - 2015-04-28 - Hiram)
    mkdir /hive/data/genomes/hg38/bed/lastzOrcOrc1.2016-06-03
    cd /hive/data/genomes/hg38/bed/lastzOrcOrc1.2016-06-03

    printf '# human vs Killer whale
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz
BLASTZ_M=254
# default BLASTZ_Q score matrix:
#       A     C     G     T
# A    91  -114   -31  -123
# C  -114   100  -125   -31
# G   -31  -125   100  -114
# T  -123   -31  -114    91

# TARGET: human hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CTGDIR=/hive/data/genomes/hg38/hg38.contigs.2bit
SEQ1_CTGLEN=/hive/data/genomes/hg38/hg38.contigs.chrom.sizes
SEQ1_LIFT=/hive/data/genomes/hg38/jkStuff/hg38.contigs.lift
SEQ1_CHUNK=40000000
SEQ1_LIMIT=30
SEQ1_LAP=10000

# QUERY: Killer whale orcOrc1
SEQ2_DIR=/hive/data/genomes/orcOrc1/orcOrc1.2bit
SEQ2_LEN=/hive/data/genomes/orcOrc1/chrom.sizes
SEQ2_CHUNK=20000000
SEQ2_LIMIT=5
SEQ2_LAP=0

BASE=/hive/data/genomes/hg38/bed/lastzOrcOrc1.2016-06-03
TMPDIR=/dev/shm
' > DEF

    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
        -chainMinScore=3000 -chainLinearGap=medium \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > do.log 2>&1
    # real    772m18.962s

    cat fb.hg38.chainOrcOrc1Link.txt
    # 1544655174 bases of 3049335806 (50.655%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` hg38 orcOrc1) \
       > rbest.log 2>&1 &
    #    real    529m17.865s

    # and for the swap:
    mkdir /hive/data/genomes/orcOrc1/bed/blastz.hg38.swap
    cd /hive/data/genomes/orcOrc1/bed/blastz.hg38.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/hg38/bed/lastzOrcOrc1.2016-06-03/DEF \
        -swap -chainMinScore=3000 -chainLinearGap=medium \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1 &
    #  real    128m38.587s

    cat fb.orcOrc1.chainHg38Link.txt
    # 1447157896 bases of 2249582125 (64.330%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` orcOrc1 hg38) \
	> rbest.log 2>&1
    # real    467m24.661s

#########################################################################
# LASTZ human/hg38 Gorilla/gorGor5 - (DONE - 2016-06-24 - Hiram)
    mkdir /hive/data/genomes/hg38/bed/lastzGorGor5.2016-06-24
    cd /hive/data/genomes/hg38/bed/lastzGorGor5.2016-06-24

    printf '# human vs gorilla
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz
BLASTZ_T=2
BLASTZ_O=600
BLASTZ_E=150
BLASTZ_M=254
BLASTZ_K=4500
BLASTZ_Y=15000
BLASTZ_Q=/scratch/data/blastz/human_chimp.v2.q
#       A     C     G     T
# A    90  -330  -236  -356
# C  -330   100  -318  -236
# G  -236  -318   100  -330
# T  -356  -236  -330    90

# TARGET: human hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
SEQ1_IN_CONTIGS=0

# QUERY: gorilla gorGor5
SEQ2_DIR=/hive/data/genomes/gorGor5/gorGor5.2bit
SEQ2_LEN=/hive/data/genomes/gorGor5/chrom.sizes
SEQ2_CHUNK=20000000
SEQ2_LAP=0
SEQ2_LIMIT=50

BASE=/hive/data/genomes/hg38/bed/lastzGorGor5.2016-06-24
TMPDIR=/dev/shm
' > DEF

    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
        -chainMinScore=3000 -chainLinearGap=medium \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > do.log 2>&1
    # real    830m35.387s

    cat fb.hg38.chainGorGor5Link.txt
    # 2887457436 bases of 3049335806 (94.691%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` hg38 gorGor5) \
        > rbest.log 2>&1 &
    # real    101m55.329s
    # load up the recip best chainNet tables
    time (doRecipBest.pl -load -continue=load -workhorse=hgwdev \
	-buildDir=`pwd` hg38 gorGor5) > loadRBest.log 2>&1 &
    cat fb.hg38.chainRBestGorGor5Link.txt
    # 2708011335 bases of 3049335806 (88.807%) in intersection

    # create and load up syntenic chainNet: 2017-10-27
cd /hive/data/genomes/hg38/bed/lastzGorGor5.2016-06-24/axtChain
netToAxt hg38.gorGor5.syn.net.gz hg38.gorGor5.all.chain.gz \
/scratch/data/hg38/hg38.2bit /hive/data/genomes/gorGor5/gorGor5.2bit stdout \
  | axtSort stdin stdout \
     | axtToChain stdin /hive/data/genomes/hg38/chrom.sizes \
        /hive/data/genomes/gorGor5/chrom.sizes stdout \
            | gzip -c > hg38.gorGor5.syn.chain.gz
hgLoadChain -tIndex hg38 chainSynGorGor5 hg38.gorGor5.syn.chain.gz
netFilter -minGap=10 hg38.gorGor5.syn.net.gz \
  | hgLoadNet -verbose=0 hg38 netSynGorGor5 stdin
cd /hive/data/genomes/hg38/bed/lastzGorGor5.2016-06-24
featureBits hg38 chainSynGorGor5Link > fb.hg38.chainSynGorGor5Link.txt 2>&1
cat fb.hg38.chainSynGorGor5Link.txt
# 2868720234 bases of 3049335806 (94.077%) in intersection

    # and for the swap:
    mkdir /hive/data/genomes/gorGor5/bed/blastz.hg38.swap
    cd /hive/data/genomes/gorGor5/bed/blastz.hg38.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/hg38/bed/lastzGorGor5.2016-06-24/DEF \
        -swap -chainMinScore=3000 -chainLinearGap=medium \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    #  real    101m50.285s

    cat fb.gorGor5.chainHg38Link.txt
    # 2766345777 bases of 3080431298 (89.804%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` gorGor5 hg38) \
       > rbest.log 2>&1
    # real    125m35.459s

###########################################################################
# Chimp Lastz run (DONE - 2016-08-03 - Hiram)
    screen -S hg38PanTro5      # use a screen to manage this longish running job
    mkdir /hive/data/genomes/hg38/bed/lastzPanTro5.2016-08-03
    cd /hive/data/genomes/hg38/bed/lastzPanTro5.2016-08-03

    # always set the BLASTZ program so we know what version was used
    printf "# human vs chimp
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz
BLASTZ_T=2
BLASTZ_O=600
BLASTZ_E=150
BLASTZ_M=254
BLASTZ_K=4500
BLASTZ_L=4500
BLASTZ_Y=15000
BLASTZ_Q=/scratch/data/blastz/human_chimp.v2.q
#    A    C    G    T
#    90 -330 -236 -356
#  -330  100 -318 -236
#  -236 -318  100 -330
#  -356 -236 -330   90

# TARGET: Human Hg38
SEQ1_DIR=/scratch/data/hg38/hg38.2bit
SEQ1_LEN=/scratch/data/hg38/chrom.sizes
SEQ1_CHUNK=40000000
SEQ1_LAP=10000
SEQ1_IN_CONTIGS=0

# QUERY: Chimp PanTro5
SEQ2_DIR=/hive/data/genomes/panTro5/panTro5.2bit
SEQ2_LEN=/hive/data/genomes/panTro5/chrom.sizes
SEQ2_CHUNK=20000000
SEQ2_LAP=0
SEQ2_LIMIT=100
SEQ2_IN_CONTIGS=0

BASE=/hive/data/genomes/hg38/bed/lastzPanTro5.2016-08-03
TMPDIR=/dev/shm
" > DEF

    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
        -chainMinScore=5000 -chainLinearGap=medium \
        -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
        -syntenicNet) > do.log 2>&1
    # real    209m31.431s

    cat fb.hg38.chainPanTro5Link.txt
    # 2907702790 bases of 3049335806 (95.355%) in intersection

    # filter with doRecipBest.pl
    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` \
        hg38 panTro5) > rbest.log 2>&1
    # real    195m53.750s

    time ($HOME/kent/src/hg/utils/automation/doRecipBest.pl -load -continue=load -workhorse=hgwdev -buildDir=`pwd` hg38 panTro5) \
	> loadRBest.log 2>&1
    # real    2m36.993s

    cat fb.hg38.chainRBestPanTro5Link.txt
    # 2737882959 bases of 3049335806 (89.786%) in intersection

    # create and load up syntenic chainNet: 2017-10-27
cd /hive/data/genomes/hg38/bed/lastzPanTro5.2016-08-03/axtChain

netToAxt hg38.panTro5.syn.net.gz hg38.panTro5.all.chain.gz \
 /scratch/data/hg38/hg38.2bit /hive/data/genomes/panTro5/panTro5.2bit stdout \
  | axtSort stdin stdout \
    | axtToChain stdin /hive/data/genomes/hg38/chrom.sizes \
        /hive/data/genomes/panTro5/chrom.sizes stdout \
            | gzip -c > hg38.panTro5.syn.chain.gz
   # real    3m23.632s

hgLoadChain -tIndex hg38 chainSynPanTro5 hg38.panTro5.syn.chain.gz
netFilter -minGap=10 hg38.panTro5.syn.net.gz \
| hgLoadNet -verbose=0 hg38 netSynPanTro5 stdin
   # real    1m13.380s

cd /hive/data/genomes/hg38/bed/lastzPanTro5.2016-08-03
featureBits hg38 chainSynPanTro5Link >&fb.hg38.chainSynPanTro5Link.txt
cat fb.hg38.chainSynPanTro5Link.txt
    # 2878970238 bases of 3049335806 (94.413%) in intersection


    # running the swap
    mkdir /hive/data/genomes/panTro5/bed/blastz.hg38.swap
    cd /hive/data/genomes/panTro5/bed/blastz.hg38.swap
    time (doBlastzChainNet.pl -verbose=2 \
        -swap /hive/data/genomes/hg38/bed/lastzPanTro5.2016-08-03/DEF \
        -chainMinScore=5000 -chainLinearGap=medium \
        -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
        -syntenicNet) > swap.log 2>&1
    # real    126m8.214s

    cat fb.panTro5.chainHg38Link.txt
    # 2935702060 bases of 3132620660 (93.714%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` \
        panTro5 hg38) > rbest.log 2>&1
    # real    240m25.264s

#############################################################################
# Chlorocebus sabaeus/Green monkey Lastz run (DONE - 2014-07-11 - Hiram)
    screen -S hg38ChlSab2      # use a screen to manage this longish running job
    mkdir /hive/data/genomes/hg38/bed/lastzChlSab2.2014-07-11
    cd /hive/data/genomes/hg38/bed/lastzChlSab2.2014-07-11

    # always set the BLASTZ program so we know what version was used
    printf "# human vs Chlorocebus sabaeus
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.52/bin/lastz
# maximum M allowed with lastz is only 254
BLASTZ_M=254
BLASTZ_Q=/scratch/data/blastz/human_chimp.v2.q
BLASTZ_O=600
BLASTZ_E=150
# other parameters from panTro2 vs hg18 lastz on advice from Webb
BLASTZ_K=4500
BLASTZ_Y=15000
BLASTZ_T=2


# TARGET: Human Hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CTGDIR=/hive/data/genomes/hg38/hg38.contigs.2bit
SEQ1_CTGLEN=/hive/data/genomes/hg38/hg38.contigs.chrom.sizes
SEQ1_LIFT=/hive/data/genomes/hg38/jkStuff/hg38.contigs.lift
SEQ1_CHUNK=20000000
SEQ1_LAP=10000

# QUERY Chlorocebus sabaeus chlSab2
SEQ2_DIR=/hive/data/genomes/chlSab2/chlSab2.2bit
SEQ2_LEN=/hive/data/genomes/chlSab2/chrom.sizes
SEQ2_CHUNK=20000000
SEQ2_LAP=0
SEQ2_IN_CONTIGS=0

BASE=/hive/data/genomes/hg38/bed/lastzChlSab2.2014-07-11
TMPDIR=/dev/shm
" > DEF

    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
        -chainMinScore=5000 -chainLinearGap=medium \
        -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
        -syntenicNet) > do.log 2>&1
    # Elapsed time: 142m4s

    cat fb.hg38.chainChlSab2Link.txt
    # 2573435303 bases of 3049335806 (84.393%) in intersection

    # filter with doRecipBest.pl
    doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` \
        hg38 chlSab2

    time (doRecipBest.pl -load -continue=load -workhorse=hgwdev \
	-buildDir=`pwd` hg38 chlSab2) > loadRBest.log 2>&1 &
    cat fb.hg38.chainRBestChlSab2Link.txt
    # 2397287473 bases of 3049335806 (78.617%) in intersection

    # create and load up syntenic chainNet: 2017-10-27
cd /hive/data/genomes/hg38/bed/lastzChlSab2.2014-07-11/axtChain
netToAxt hg38.chlSab2.syn.net.gz hg38.chlSab2.all.chain.gz \
/scratch/data/hg38/hg38.2bit /hive/data/genomes/chlSab2/chlSab2.2bit stdout \
  | axtSort stdin stdout \
     | axtToChain stdin /hive/data/genomes/hg38/chrom.sizes \
        /hive/data/genomes/chlSab2/chrom.sizes stdout \
            | gzip -c > hg38.chlSab2.syn.chain.gz
hgLoadChain -tIndex hg38 chainSynChlSab2 hg38.chlSab2.syn.chain.gz
netFilter -minGap=10 hg38.chlSab2.syn.net.gz \
  | hgLoadNet -verbose=0 hg38 netSynChlSab2 stdin
cd /hive/data/genomes/hg38/bed/lastzChlSab2.2014-07-11
featureBits hg38 chainSynChlSab2Link > fb.hg38.chainSynChlSab2Link.txt 2>&1
cat fb.hg38.chainSynChlSab2Link.txt
# 2537786701 bases of 3049335806 (83.224%) in intersection

    # running the swap
    mkdir /hive/data/genomes/chlSab2/bed/blastz.hg38.swap
    cd /hive/data/genomes/chlSab2/bed/blastz.hg38.swap
    time (doBlastzChainNet.pl -verbose=2 \
        -swap /hive/data/genomes/hg38/bed/lastzChlSab2.2014-07-11/DEF \
        -chainMinScore=5000 -chainLinearGap=medium \
        -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
        -syntenicNet) > swap.log 2>&1
    # Elapsed time: 88m48s

    cat fb.chlSab2.chainHg38Link.txt
    # 2429053010 bases of 2752019208 (88.264%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` \
        chlSab2 hg38) > rbest.log 2>&1
    # real    240m25.264s

#############################################################################
# LASTZ human/hg38 vs. turkey/melGal5 - (DONE - 2017-01-20 - Hiram)
    mkdir /hive/data/genomes/hg38/bed/lastzMelGal5.2017-01-20
    cd /hive/data/genomes/hg38/bed/lastzMelGal5.2017-01-20

    printf '# human vs turkey
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz
BLASTZ_O=400
BLASTZ_E=30
BLASTZ_Y=3400
BLASTZ_L=6000
BLASTZ_K=2200
BLASTZ_M=50
BLASTZ_Q=/scratch/data/blastz/HoxD55.q
#      A    C    G    T
#     91  -90  -25 -100
#    -90  100 -100  -25
#    -25 -100  100  -90
#   -100  -25  -90  91

# TARGET: human hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CTGDIR=/hive/data/genomes/hg38/hg38.contigs.2bit
SEQ1_CTGLEN=/hive/data/genomes/hg38/hg38.contigs.chrom.sizes
SEQ1_LIFT=/hive/data/genomes/hg38/jkStuff/hg38.contigs.lift
SEQ1_CHUNK=40000000
SEQ1_LIMIT=30
SEQ1_LAP=10000

# QUERY: turkey melGal5
SEQ2_DIR=/hive/data/genomes/melGal5/melGal5.2bit
SEQ2_LEN=/hive/data/genomes/melGal5/chrom.sizes
SEQ2_CHUNK=20000000
SEQ2_LIMIT=300
SEQ2_LAP=0

BASE=/hive/data/genomes/hg38/bed/lastzMelGal5.2017-01-20
TMPDIR=/dev/shm
' > DEF

    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
        -chainMinScore=5000 -chainLinearGap=loose \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > do.log 2>&1
    # real    190m58.492s

    cat fb.hg38.chainMelGal5Link.txt
    # 135950364 bases of 3049335806 (4.458%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` hg38 melGal5) \
      > rbest.log 2>&1 &
    # real    492m55.893s

    # and for the swap:
    mkdir /hive/data/genomes/melGal5/bed/blastz.hg38.swap
    cd /hive/data/genomes/melGal5/bed/blastz.hg38.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/hg38/bed/lastzMelGal5.2017-01-20/DEF \
        -swap -chainMinScore=5000 -chainLinearGap=loose \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    #  real    36m37.471s

    cat fb.melGal5.chainHg38Link.txt
    # 107549251 bases of 1093044709 (9.839%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` melGal5 hg38) \
        > rbest.log 2>&1
    # real    456m25.214s

#########################################################################
# LASTZ human/hg38 vs. brown kiwi/aptMan1 - (DONE - 2017-02-21 - Hiram)
    mkdir /hive/data/genomes/hg38/bed/lastzAptMan1.2017-02-21
    cd /hive/data/genomes/hg38/bed/lastzAptMan1.2017-02-21

    printf '# human vs brown kiwi
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz
BLASTZ_O=400
BLASTZ_E=30
BLASTZ_Y=3400
BLASTZ_L=6000
BLASTZ_K=2200
BLASTZ_M=50
BLASTZ_Q=/scratch/data/blastz/HoxD55.q
#      A    C    G    T
#     91  -90  -25 -100
#    -90  100 -100  -25
#    -25 -100  100  -90
#   -100  -25  -90  91

# TARGET: human hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CTGDIR=/hive/data/genomes/hg38/hg38.contigs.2bit
SEQ1_CTGLEN=/hive/data/genomes/hg38/hg38.contigs.chrom.sizes
SEQ1_LIFT=/hive/data/genomes/hg38/jkStuff/hg38.contigs.lift
SEQ1_CHUNK=40000000
SEQ1_LIMIT=30
SEQ1_LAP=10000

# QUERY: brown kiwi aptMan1
SEQ2_DIR=/hive/data/genomes/aptMan1/aptMan1.2bit
SEQ2_LEN=/hive/data/genomes/aptMan1/chrom.sizes
SEQ2_CHUNK=20000000
SEQ2_LIMIT=40
SEQ2_LAP=0

BASE=/hive/data/genomes/hg38/bed/lastzAptMan1.2017-02-21
TMPDIR=/dev/shm
" > DEF

    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
        -chainMinScore=5000 -chainLinearGap=loose \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > do.log 2>&1
    # real    368m59.939s

    cat fb.hg38.chainAptMan1Link.txt
    # 150901346 bases of 3049335806 (4.949%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` hg38 aptMan1) \
         > rbest.log 2>&1 &
    # real    300m28.333s

    # and for the swap:
    mkdir /hive/data/genomes/aptMan1/bed/blastz.hg38.swap
    cd /hive/data/genomes/aptMan1/bed/blastz.hg38.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/hg38/bed/lastzAptMan1.2017-02-21/DEF \
        -swap -chainMinScore=5000 -chainLinearGap=loose \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    #  real    16m9.761s

    cat fb.aptMan1.chainHg38Link.txt
    # 125964464 bases of 1311306859 (9.606%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` aptMan1 hg38) \
          > rbest.log 2>&1
    # real    269m10.012s

#########################################################################
# LASTZ human/hg38 Tree dolphin/turTru2 - (DONE - 2017-02-21 - Hiram)
    mkdir /hive/data/genomes/hg38/bed/lastzTurTru2.2017-02-21
    cd /hive/data/genomes/hg38/bed/lastzTurTru2.2017-02-21

    printf '# human vs dolphin
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz

# TARGET: Human Hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CTGDIR=/hive/data/genomes/hg38/hg38.contigs.2bit
SEQ1_CTGLEN=/hive/data/genomes/hg38/hg38.contigs.chrom.sizes
SEQ1_LIFT=/hive/data/genomes/hg38/jkStuff/hg38.contigs.lift
SEQ1_CHUNK=20000000
SEQ1_LAP=10000

# QUERY: Dog TurTru2
SEQ2_DIR=/hive/data/genomes/turTru2/turTru2.2bit
SEQ2_LEN=/hive/data/genomes/turTru2/chrom.sizes
SEQ2_CHUNK=20000000
SEQ2_LIMIT=600
SEQ2_LAP=0

BASE=/hive/data/genomes/hg38/bed/lastzTurTru2.2017-02-21
TMPDIR=/dev/shm
' > DEF

    time (doBlastzChainNet.pl -verbose=2 `pwd`/DEF \
        -syntenicNet -workhorse=hgwdev -smallClusterHub=ku \
          -bigClusterHub=ku -fileServer=hgwdev \
             -chainMinScore=3000 -chainLinearGap=medium) > do.log 2>&1
    # real    572m54.888s

    cat fb.hg38.chainTurTru2Link.txt
    # 1516482527 bases of 3049335806 (49.732%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` hg38 turTru2) \
      > rbest.log 2>&1 &
    # real    1079m31.677s

    # and for the swap:
    mkdir /hive/data/genomes/turTru2/bed/blastz.hg38.swap
    cd /hive/data/genomes/turTru2/bed/blastz.hg38.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/hg38/bed/lastzTurTru2.2017-02-21/DEF \
        -swap -chainMinScore=3000 -chainLinearGap=medium \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    #  real    228m9.744s

    cat fb.turTru2.chainHg38Link.txt
    # 1432042877 bases of 2332402443 (61.398%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` turTru2 hg38) \
          > rbest.log 2>&1
    # real    1295m48.357s

#########################################################################
# LASTZ human/hg38 vs. platypus/ornAna2 - (DONE - 2017-02-21 - Hiram)
    mkdir /hive/data/genomes/hg38/bed/lastzOrnAna2.2017-02-21
    cd /hive/data/genomes/hg38/bed/lastzOrnAna2.2017-02-21

    printf '# human vs platypus
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz
BLASTZ_O=400
BLASTZ_E=30
BLASTZ_Y=3400
BLASTZ_L=6000
BLASTZ_K=2200
BLASTZ_M=50
BLASTZ_Q=/scratch/data/blastz/HoxD55.q
#      A    C    G    T
#     91  -90  -25 -100
#    -90  100 -100  -25
#    -25 -100  100  -90
#   -100  -25  -90  91

# TARGET: human hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CTGDIR=/hive/data/genomes/hg38/hg38.contigs.2bit
SEQ1_CTGLEN=/hive/data/genomes/hg38/hg38.contigs.chrom.sizes
SEQ1_LIFT=/hive/data/genomes/hg38/jkStuff/hg38.contigs.lift
SEQ1_CHUNK=40000000
SEQ1_LIMIT=30
SEQ1_LAP=10000

# QUERY: platypus ornAna2
SEQ2_DIR=/hive/data/genomes/ornAna2/ornAna2.2bit
SEQ2_LEN=/hive/data/genomes/ornAna2/chrom.sizes
SEQ2_CHUNK=20000000
SEQ2_LIMIT=300
SEQ2_LAP=0

BASE=/hive/data/genomes/hg38/bed/lastzOrnAna2.2017-02-21
TMPDIR=/dev/shm
' > DEF

    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
        -chainMinScore=5000 -chainLinearGap=loose \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > do.log 2>&1
    # real    445m13.234s

    cat fb.hg38.chainOrnAna2Link.txt
    # 256721472 bases of 3049335806 (8.419%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` hg38 ornAna2) \
      > rbest.log 2>&1 &
    # real    788m25.199s

    # and for the swap:
    mkdir /hive/data/genomes/ornAna2/bed/blastz.hg38.swap
    cd /hive/data/genomes/ornAna2/bed/blastz.hg38.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/hg38/bed/lastzOrnAna2.2017-02-21/DEF \
        -swap -chainMinScore=5000 -chainLinearGap=loose \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    #  real    130m42.942s

    cat fb.ornAna2.chainHg38Link.txt
    # 232286308 bases of 1842252119 (12.609%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` ornAna2 hg38) \
          > rbest.log 2>&1
    # real    821m10.828s

#############################################################################
# Colobus angolensis palliatus/Angolan colobus lastz run (DONE - 2017-02-27 - Hiram)
    screen -S hg38ColAng1      # use a screen to manage this longish running job
    mkdir /hive/data/genomes/hg38/bed/lastzColAng1.2017-02-27
    cd /hive/data/genomes/hg38/bed/lastzColAng1.2017-02-27

    # always set the BLASTZ program so we know what version was used
    printf "# human vs Angolan colobus
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz
# maximum M allowed with lastz is only 254
BLASTZ_M=254
BLASTZ_Q=/scratch/data/blastz/human_chimp.v2.q
BLASTZ_O=600
BLASTZ_E=150
# other parameters from panTro2 vs hg18 lastz on advice from Webb
BLASTZ_K=4500
BLASTZ_Y=15000
BLASTZ_T=2


# TARGET: Human Hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CTGDIR=/hive/data/genomes/hg38/hg38.contigs.2bit
SEQ1_CTGLEN=/hive/data/genomes/hg38/hg38.contigs.chrom.sizes
SEQ1_LIFT=/hive/data/genomes/hg38/jkStuff/hg38.contigs.lift
SEQ1_CHUNK=20000000
SEQ1_LAP=10000

# QUERY Angolan colobus colAng1
SEQ2_DIR=/hive/data/genomes/colAng1/colAng1.2bit
SEQ2_LEN=/hive/data/genomes/colAng1/chrom.sizes
SEQ2_CHUNK=20000000
SEQ2_LAP=0
SEQ2_LIMIT=40
SEQ2_IN_CONTIGS=0

BASE=/hive/data/genomes/hg38/bed/lastzColAng1.2017-02-27
TMPDIR=/dev/shm
" > DEF

    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
        -chainMinScore=5000 -chainLinearGap=medium \
         -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
          -syntenicNet) > do.log 2>&1
    # real    123m41.958s

    cat fb.hg38.chainColAng1Link.txt
    # 2489504237 bases of 3049335806 (81.641%) in intersection

    # filter with doRecipBest.pl
    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` \
        hg38 colAng1) > rbest.log 2>&1
    # real    240m0.041s
    time (doRecipBest.pl -load -continue=load -workhorse=hgwdev \
	-buildDir=`pwd` hg38 colAng1) > loadRBest.log 2>&1 &
    cat fb.hg38.chainRBestColAng1Link.txt
    # 2323958368 bases of 3049335806 (76.212%) in intersection

    # create and load up syntenic chainNet: 2017-10-27

cd /hive/data/genomes/hg38/bed/lastzColAng1.2017-02-27/axtChain
netToAxt hg38.colAng1.syn.net.gz hg38.colAng1.all.chain.gz \
/scratch/data/hg38/hg38.2bit /hive/data/genomes/colAng1/colAng1.2bit stdout \
  | axtSort stdin stdout \
     | axtToChain stdin /hive/data/genomes/hg38/chrom.sizes \
        /hive/data/genomes/colAng1/chrom.sizes stdout \
            | gzip -c > hg38.colAng1.syn.chain.gz
hgLoadChain -tIndex hg38 chainSynColAng1 hg38.colAng1.syn.chain.gz
netFilter -minGap=10 hg38.colAng1.syn.net.gz \
  | hgLoadNet -verbose=0 hg38 netSynColAng1 stdin
cd /hive/data/genomes/hg38/bed/lastzColAng1.2017-02-27
featureBits hg38 chainSynColAng1Link > fb.hg38.chainSynColAng1Link.txt 2>&1
cat fb.hg38.chainSynColAng1Link.txt
# 2439773865 bases of 3049335806 (80.010%) in intersection

    # running the swap
    mkdir /hive/data/genomes/colAng1/bed/blastz.hg38.swap
    cd /hive/data/genomes/colAng1/bed/blastz.hg38.swap
    time (doBlastzChainNet.pl -verbose=2 \
        -swap /hive/data/genomes/hg38/bed/lastzColAng1.2017-02-27/DEF \
        -chainMinScore=5000 -chainLinearGap=medium \
        -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
        -syntenicNet) > swap.log 2>&1
    # real    80m23.924s

    cat fb.colAng1.chainHg38Link.txt
    # 2355021477 bases of 2679973137 (87.875%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` \
        colAng1 hg38) > rbest.log 2>&1
    # real    224m29.002s

#############################################################################
# Macaca nemestrina/pig-tailed macaque lastz run (DONE - 2017-02-27 - Hiram)
    screen -S hg38MacNem1      # use a screen to manage this longish running job
    mkdir /hive/data/genomes/hg38/bed/lastzMacNem1.2017-02-27
    cd /hive/data/genomes/hg38/bed/lastzMacNem1.2017-02-27

    # always set the BLASTZ program so we know what version was used
    printf "# human vs pig-tailed macaque
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz
# maximum M allowed with lastz is only 254
BLASTZ_M=254
BLASTZ_Q=/scratch/data/blastz/human_chimp.v2.q
BLASTZ_O=600
BLASTZ_E=150
# other parameters from panTro2 vs hg18 lastz on advice from Webb
BLASTZ_K=4500
BLASTZ_Y=15000
BLASTZ_T=2


# TARGET: Human Hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CTGDIR=/hive/data/genomes/hg38/hg38.contigs.2bit
SEQ1_CTGLEN=/hive/data/genomes/hg38/hg38.contigs.chrom.sizes
SEQ1_LIFT=/hive/data/genomes/hg38/jkStuff/hg38.contigs.lift
SEQ1_CHUNK=20000000
SEQ1_LAP=10000

# QUERY pig-tailed macaque macNem1
SEQ2_DIR=/hive/data/genomes/macNem1/macNem1.2bit
SEQ2_LEN=/hive/data/genomes/macNem1/chrom.sizes
SEQ2_CHUNK=20000000
SEQ2_LAP=0
SEQ2_LIMIT=40
SEQ2_IN_CONTIGS=0

BASE=/hive/data/genomes/hg38/bed/lastzMacNem1.2017-02-27
TMPDIR=/dev/shm
" > DEF

    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
        -chainMinScore=5000 -chainLinearGap=medium \
         -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
          -syntenicNet) > do.log 2>&1
    # real    122m14.198s

    cat fb.hg38.chainMacNem1Link.txt
    # 2546912844 bases of 3049335806 (83.524%) in intersection

    # filter with doRecipBest.pl
    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` \
        hg38 macNem1) > rbest.log 2>&1
    # real    201m54.795s
    time (doRecipBest.pl -load -continue=load -workhorse=hgwdev \
	-buildDir=`pwd` hg38 macNem1) > loadRBest.log 2>&1 &
    cat fb.hg38.chainRBestMacNem1Link.txt
    # 2376010543 bases of 3049335806 (77.919%) in intersection

    # create and load up syntenic chainNet: 2017-10-27
cd /hive/data/genomes/hg38/bed/lastzMacNem1.2017-02-27/axtChain
netToAxt hg38.macNem1.syn.net.gz hg38.macNem1.all.chain.gz \
/scratch/data/hg38/hg38.2bit /hive/data/genomes/macNem1/macNem1.2bit stdout \
  | axtSort stdin stdout \
     | axtToChain stdin /hive/data/genomes/hg38/chrom.sizes \
        /hive/data/genomes/macNem1/chrom.sizes stdout \
            | gzip -c > hg38.macNem1.syn.chain.gz
hgLoadChain -tIndex hg38 chainSynMacNem1 hg38.macNem1.syn.chain.gz
netFilter -minGap=10 hg38.macNem1.syn.net.gz \
  | hgLoadNet -verbose=0 hg38 netSynMacNem1 stdin
cd /hive/data/genomes/hg38/bed/lastzMacNem1.2017-02-27
featureBits hg38 chainSynMacNem1Link > fb.hg38.chainSynMacNem1Link.txt 2>&1
cat fb.hg38.chainSynMacNem1Link.txt
# 2505548649 bases of 3049335806 (82.167%) in intersection

    # running the swap
    mkdir /hive/data/genomes/macNem1/bed/blastz.hg38.swap
    cd /hive/data/genomes/macNem1/bed/blastz.hg38.swap
    time (doBlastzChainNet.pl -verbose=2 \
        -swap /hive/data/genomes/hg38/bed/lastzMacNem1.2017-02-27/DEF \
        -chainMinScore=5000 -chainLinearGap=medium \
        -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
        -syntenicNet) > swap.log 2>&1
    # real    82m42.545s

    cat fb.macNem1.chainHg38Link.txt
    # 2424148087 bases of 2838503083 (85.402%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` \
        macNem1 hg38) > rbest.log 2>&1
    # real    239m15.997s

#############################################################################
# LASTZ human/hg38 Mouse lemur/micMur3 - (DONE - 2017-03-03 - Hiram)
    mkdir /hive/data/genomes/hg38/bed/lastzMicMur3.2017-03-03
    cd /hive/data/genomes/hg38/bed/lastzMicMur3.2017-03-03

    printf '# human vs Mouse lemur
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz
# maximum M allowed with lastz is only 254
BLASTZ_M=254
BLASTZ_Q=/scratch/data/blastz/human_chimp.v2.q
BLASTZ_O=600
BLASTZ_E=150
# other parameters from panTro2 vs hg18 lastz on advice from Webb
BLASTZ_K=4500
BLASTZ_Y=15000
BLASTZ_T=2

# TARGET: human hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CTGDIR=/hive/data/genomes/hg38/hg38.contigs.2bit
SEQ1_CTGLEN=/hive/data/genomes/hg38/hg38.contigs.chrom.sizes
SEQ1_LIFT=/hive/data/genomes/hg38/jkStuff/hg38.contigs.lift
SEQ1_CHUNK=40000000
SEQ1_LIMIT=10
SEQ1_LAP=10000

# QUERY: Mouse lemur micMur3
SEQ2_DIR=/hive/data/genomes/micMur3/micMur3.2bit
SEQ2_LEN=/hive/data/genomes/micMur3/chrom.sizes
SEQ2_CHUNK=20000000
SEQ2_LIMIT=20
SEQ2_LAP=0

BASE=/hive/data/genomes/hg38/bed/lastzMicMur3.2017-03-03
TMPDIR=/dev/shm
' > DEF


    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
        -chainMinScore=3000 -chainLinearGap=medium \
          -workhorse=hgwdev -smallClusterHub=ku \
            -bigClusterHub=ku -syntenicNet) > do.log 2>&1
    # real    1149m34.034s

    cat fb.hg38.chainMicMur3Link.txt
    # 906521007 bases of 3049335806 (29.728%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` hg38 micMur3) \
          > rbest.log 2>&1 &
    # real    265m38.806s
    time (doRecipBest.pl -load -continue=load -workhorse=hgwdev \
	-buildDir=`pwd` hg38 micMur3) > rbest.log 2>&1 &
    cat fb.hg38.chainRBestMicMur3Link.txt
    # 857684217 bases of 3049335806 (28.127%) in intersection

    # create and load up syntenic chainNet: 2017-10-27
cd /hive/data/genomes/hg38/bed/lastzMicMur3.2017-03-03/axtChain
netToAxt hg38.micMur3.syn.net.gz hg38.micMur3.all.chain.gz \
/scratch/data/hg38/hg38.2bit /hive/data/genomes/micMur3/micMur3.2bit stdout \
  | axtSort stdin stdout \
     | axtToChain stdin /hive/data/genomes/hg38/chrom.sizes \
        /hive/data/genomes/micMur3/chrom.sizes stdout \
            | gzip -c > hg38.micMur3.syn.chain.gz
hgLoadChain -tIndex hg38 chainSynMicMur3 hg38.micMur3.syn.chain.gz
netFilter -minGap=10 hg38.micMur3.syn.net.gz \
  | hgLoadNet -verbose=0 hg38 netSynMicMur3 stdin
cd /hive/data/genomes/hg38/bed/lastzMicMur3.2017-03-03
featureBits hg38 chainSynMicMur3Link > fb.hg38.chainSynMicMur3Link.txt 2>&1
cat fb.hg38.chainSynMicMur3Link.txt
# 874918179 bases of 3049335806 (28.692%) in intersection

    # and for the swap:
    mkdir /hive/data/genomes/micMur3/bed/blastz.hg38.swap
    cd /hive/data/genomes/micMur3/bed/blastz.hg38.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/hg38/bed/lastzMicMur3.2017-03-03/DEF \
        -swap -chainMinScore=3000 -chainLinearGap=medium \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    #  real    42m21.629s

    cat fb.micMur3.chainHg38Link.txt
    # 880636728 bases of 2386321975 (36.904%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` micMur3 hg38) \
      > rbest.log 2>&1
    # real    296m23.384s

#########################################################################
# LASTZ human/hg38 Chinese pangolin/manPen1 - (DONE - 2017-03-15 - Hiram)
    mkdir /hive/data/genomes/hg38/bed/lastzManPen1.2017-03-15
    cd /hive/data/genomes/hg38/bed/lastzManPen1.2017-03-15

    printf '# human vs Chinese pangolin
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz

# TARGET: human hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CTGDIR=/hive/data/genomes/hg38/hg38.contigs.2bit
SEQ1_CTGLEN=/hive/data/genomes/hg38/hg38.contigs.chrom.sizes
SEQ1_LIFT=/hive/data/genomes/hg38/jkStuff/hg38.contigs.lift
SEQ1_CHUNK=40000000
SEQ1_LIMIT=30
SEQ1_LAP=10000

# QUERY: Chinese pangolin manPen1
SEQ2_DIR=/hive/data/genomes/manPen1/manPen1.2bit
SEQ2_LEN=/hive/data/genomes/manPen1/chrom.sizes
SEQ2_CHUNK=20000000
SEQ2_LIMIT=120
SEQ2_LAP=0

BASE=/hive/data/genomes/hg38/bed/lastzManPen1.2017-03-15
TMPDIR=/dev/shm
' > DEF

    time (doBlastzChainNet.pl -verbose=2 `pwd`/DEF \
        -syntenicNet -fileServer=hgwdev \
        -chainMinScore=3000 -chainLinearGap=medium \
        -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku) > do.log 2>&1
    # real    495m29.451s

    cat fb.hg38.chainManPen1Link.txt
    # 1373891126 bases of 3049335806 (45.055%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` hg38 manPen1) \
          > rbest.log 2>&1 &
    # real    672m29.761s

    # and for the swap:
    mkdir /hive/data/genomes/manPen1/bed/blastz.hg38.swap
    cd /hive/data/genomes/manPen1/bed/blastz.hg38.swap

    time (doBlastzChainNet.pl -verbose=2 -swap \
        /hive/data/genomes/hg38/bed/lastzManPen1.2017-03-15/DEF \
        -syntenicNet -fileServer=hgwdev \
        -chainMinScore=3000 -chainLinearGap=medium \
        -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku) > swap.log 2>&1
    #  real    122m34.841s

    cat fb.manPen1.chainHg38Link.txt
    # 1305035790 bases of 1999066070 (65.282%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` manPen1 hg38) \
      > rbest.log 2>&1
    # real    729m45.645s

#########################################################################
# LASTZ human/hg38 vs. Golden eagle/aquChr2 - (DONE - 2017-03-16 - Hiram)
    mkdir /hive/data/genomes/hg38/bed/lastzAquChr2.2017-03-16
    cd /hive/data/genomes/hg38/bed/lastzAquChr2.2017-03-16

    printf "# human vs Golden eagle
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz
BLASTZ_O=400
BLASTZ_E=30
BLASTZ_Y=3400
BLASTZ_L=6000
BLASTZ_K=2200
BLASTZ_M=50
BLASTZ_Q=/scratch/data/blastz/HoxD55.q
#      A    C    G    T
#     91  -90  -25 -100
#    -90  100 -100  -25
#    -25 -100  100  -90
#   -100  -25  -90  91

# TARGET: human hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CTGDIR=/hive/data/genomes/hg38/hg38.contigs.2bit
SEQ1_CTGLEN=/hive/data/genomes/hg38/hg38.contigs.chrom.sizes
SEQ1_LIFT=/hive/data/genomes/hg38/jkStuff/hg38.contigs.lift
SEQ1_CHUNK=40000000
SEQ1_LIMIT=30
SEQ1_LAP=10000

# QUERY: Golden eagle aquChr2
SEQ2_DIR=/hive/data/genomes/aquChr2/aquChr2.2bit
SEQ2_LEN=/hive/data/genomes/aquChr2/chrom.sizes
SEQ2_CHUNK=20000000
SEQ2_LIMIT=30
SEQ2_LAP=0

BASE=/hive/data/genomes/hg38/bed/lastzAquChr2.2017-03-16
TMPDIR=/dev/shm
" > DEF
    # << happy emacs

    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
        -chainMinScore=5000 -chainLinearGap=loose \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > do.log 2>&1
    # real    249m22.348s

    cat fb.hg38.chainAquChr2Link.txt
    # 168168136 bases of 3049335806 (5.515%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` hg38 aquChr2) \
       > rbest.log 2>&1 &
    # real    288m36.217s

    # and for the swap:
    mkdir /hive/data/genomes/aquChr2/bed/blastz.hg38.swap
    cd /hive/data/genomes/aquChr2/bed/blastz.hg38.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/hg38/bed/lastzAquChr2.2017-03-16/DEF \
        -swap -chainMinScore=5000 -chainLinearGap=loose \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    #  real    14m18.710s

    cat fb.aquChr2.chainHg38Link.txt
    # 127935996 bases of 1180019022 (10.842%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` aquChr2 hg38) \
         > rbest.log 2>&1
    # real    180m40.655s

#########################################################################
# LASTZ Cow bisBis1 (DONE - 2017-03-17 - Hiram)
    mkdir /hive/data/genomes/hg38/bed/lastzBisBis1.2017-03-17
    cd /hive/data/genomes/hg38/bed/lastzBisBis1.2017-03-17

    printf '# human vs bison
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz
# maximum M allowed with lastz is only 254
BLASTZ_M=254

# TARGET: Human hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CTGDIR=/hive/data/genomes/hg38/hg38.contigs.2bit
SEQ1_CTGLEN=/hive/data/genomes/hg38/hg38.contigs.chrom.sizes
SEQ1_LIFT=/hive/data/genomes/hg38/jkStuff/hg38.contigs.lift
SEQ1_CHUNK=40000000
SEQ1_LIMIT=30
SEQ1_LAP=10000

# QUERY: Bison bisBis1
SEQ2_DIR=/hive/data/genomes/bisBis1/bisBis1.2bit
SEQ2_LEN=/hive/data/genomes/bisBis1/chrom.sizes
SEQ2_CHUNK=20000000
SEQ2_LAP=0
SEQ2_LIMIT=100


BASE=/hive/data/genomes/hg38/bed/lastzBisBis1.2017-03-17
TMPDIR=/dev/shm
' > DEF

    time (doBlastzChainNet.pl -verbose=2 \
        `pwd`/DEF \
        -syntenicNet -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
        -chainMinScore=3000 -chainLinearGap=medium) > do.log 2>&1
    # real    686m35.655s

    cat fb.hg38.chainBisBis1Link.txt
    # 1392131211 bases of 3049335806 (45.654%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` hg38 bisBis1) \
         > rbest.log 2>&1 &
    # real    585m14.200s

    #   running the swap
    mkdir /hive/data/genomes/bisBis1/bed/blastz.hg38.swap
    cd /hive/data/genomes/bisBis1/bed/blastz.hg38.swap
    time (doBlastzChainNet.pl -verbose=2 \
        /hive/data/genomes/hg38/bed/lastzBisBis1.2017-03-17/DEF \
        -swap  -syntenicNet \
        -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
        -chainMinScore=3000 -chainLinearGap=medium) > swap.log 2>&1
    #   real    374m22.343s

    cat fb.bisBis1.chainHg38Link.txt
    #   1344953854 bases of 2757854331 (48.768%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` bisBis1 hg38) \
         > rbest.log 2>&1
    # real    828m16.502s

############################################################################
# Rhinopithecus bieti/Black snub-nosed monkey lastz run
#                              (DONE - 2017-03-23 - Hiram)
    screen -S hg38RhiBie1      # use a screen to manage this longish running job
    mkdir /hive/data/genomes/hg38/bed/lastzRhiBie1.2017-03-23
    cd /hive/data/genomes/hg38/bed/lastzRhiBie1.2017-03-23

    # always set the BLASTZ program so we know what version was used
    printf "# human vs black snub-nosed monkey
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz
# maximum M allowed with lastz is only 254
BLASTZ_M=254
BLASTZ_Q=/scratch/data/blastz/human_chimp.v2.q
BLASTZ_O=600
BLASTZ_E=150
# other parameters from panTro2 vs hg18 lastz on advice from Webb
BLASTZ_K=4500
BLASTZ_Y=15000
BLASTZ_T=2

# TARGET: Human Hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CTGDIR=/hive/data/genomes/hg38/hg38.contigs.2bit
SEQ1_CTGLEN=/hive/data/genomes/hg38/hg38.contigs.chrom.sizes
SEQ1_LIFT=/hive/data/genomes/hg38/jkStuff/hg38.contigs.lift
SEQ1_CHUNK=20000000
SEQ1_LAP=10000

# QUERY black snub-nosed monkey rhiBie1
SEQ2_DIR=/hive/data/genomes/rhiBie1/rhiBie1.2bit
SEQ2_LEN=/hive/data/genomes/rhiBie1/chrom.sizes
SEQ2_CHUNK=20000000
SEQ2_LAP=0
SEQ2_LIMIT=300
SEQ2_IN_CONTIGS=0

BASE=/hive/data/genomes/hg38/bed/lastzRhiBie1.2017-03-23
TMPDIR=/dev/shm
" > DEF

    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
        -chainMinScore=5000 -chainLinearGap=medium \
         -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
          -syntenicNet) > do.log 2>&1
    # real    156m11.384s

    cat fb.hg38.chainRhiBie1Link.txt
    # 2532928717 bases of 3049335806 (83.065%) in intersection

    # filter with doRecipBest.pl
    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` \
        hg38 rhiBie1) > rbest.log 2>&1
    # real    457m19.209s
    time (doRecipBest.pl -load -continue=load -workhorse=hgwdev \
	-buildDir=`pwd` hg38 rhiBie1) > loadRBest.log 2>&1 &
    cat fb.hg38.chainRBestRhiBie1Link.txt
    # 2356179781 bases of 3049335806 (77.269%) in intersection

    # create and load up syntenic chainNet: 2017-10-27
cd /hive/data/genomes/hg38/bed/lastzRhiBie1.2017-03-23/axtChain
netToAxt hg38.rhiBie1.syn.net.gz hg38.rhiBie1.all.chain.gz \
/scratch/data/hg38/hg38.2bit /hive/data/genomes/rhiBie1/rhiBie1.2bit stdout \
  | axtSort stdin stdout \
     | axtToChain stdin /hive/data/genomes/hg38/chrom.sizes \
        /hive/data/genomes/rhiBie1/chrom.sizes stdout \
            | gzip -c > hg38.rhiBie1.syn.chain.gz
hgLoadChain -tIndex hg38 chainSynRhiBie1 hg38.rhiBie1.syn.chain.gz
netFilter -minGap=10 hg38.rhiBie1.syn.net.gz \
  | hgLoadNet -verbose=0 hg38 netSynRhiBie1 stdin
cd /hive/data/genomes/hg38/bed/lastzRhiBie1.2017-03-23
featureBits hg38 chainSynRhiBie1Link > fb.hg38.chainSynRhiBie1Link.txt 2>&1
cat fb.hg38.chainSynRhiBie1Link.txt
# 2453690582 bases of 3049335806 (80.466%) in intersection

    # running the swap
    mkdir /hive/data/genomes/rhiBie1/bed/blastz.hg38.swap
    cd /hive/data/genomes/rhiBie1/bed/blastz.hg38.swap
    time (doBlastzChainNet.pl -verbose=2 \
        -swap /hive/data/genomes/hg38/bed/lastzRhiBie1.2017-03-23/DEF \
        -chainMinScore=5000 -chainLinearGap=medium \
        -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
        -syntenicNet) > swap.log 2>&1
    # real    125m54.338s

    cat fb.rhiBie1.chainHg38Link.txt
    # 2420545520 bases of 2977074741 (81.306%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` \
        rhiBie1 hg38) > rbest.log 2>&1
    # real    595m32.110s

#############################################################################
# LASTZ human/hg38 vs. X. tropicalis/xenTro9 - (DONE - 2017-03-29 - Hiram)
    mkdir /hive/data/genomes/hg38/bed/lastzXenTro9.2017-03-29
    cd /hive/data/genomes/hg38/bed/lastzXenTro9.2017-03-29

    printf '# human vs X. tropicalis
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz
BLASTZ_O=400
BLASTZ_E=30
BLASTZ_Y=3400
BLASTZ_L=6000
BLASTZ_K=2200
BLASTZ_M=50
BLASTZ_Q=/scratch/data/blastz/HoxD55.q
#      A    C    G    T
#     91  -90  -25 -100
#    -90  100 -100  -25
#    -25 -100  100  -90
#   -100  -25  -90  91

# TARGET: human hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CTGDIR=/hive/data/genomes/hg38/hg38.contigs.2bit
SEQ1_CTGLEN=/hive/data/genomes/hg38/hg38.contigs.chrom.sizes
SEQ1_LIFT=/hive/data/genomes/hg38/jkStuff/hg38.contigs.lift
SEQ1_CHUNK=40000000
SEQ1_LIMIT=10
SEQ1_LAP=10000

# QUERY: X. tropicalis xenTro9
SEQ2_DIR=/hive/data/genomes/xenTro9/xenTro9.2bit
SEQ2_LEN=/hive/data/genomes/xenTro9/chrom.sizes
SEQ2_CHUNK=20000000
SEQ2_LIMIT=20
SEQ2_LAP=0

BASE=/hive/data/genomes/hg38/bed/lastzXenTro9.2017-03-29
TMPDIR=/dev/shm
' > DEF

    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
        -chainMinScore=5000 -chainLinearGap=loose \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > do.log 2>&1 &
    # real    911m54.869s

    # download failed due to hgwdev home directory problem
    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
        -chainMinScore=5000 -chainLinearGap=loose \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -continue=download -syntenicNet) > download.log 2>&1 &
    # real    3m53.808s

    cat fb.hg38.chainXenTro9Link.txt
    # 117720401 bases of 3049335806 (3.861%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` hg38 xenTro9) \
       > rbest.log 2>&1 &
    # real    813m7.491s

    # and for the swap:
    mkdir /hive/data/genomes/xenTro9/bed/blastz.hg38.swap
    cd /hive/data/genomes/xenTro9/bed/blastz.hg38.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/hg38/bed/lastzXenTro9.2017-03-29/DEF \
        -swap -chainMinScore=5000 -chainLinearGap=loose \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    #  real    61m0.707s

    cat fb.xenTro9.chainHg38Link.txt
    # 108900066 bases of 1369865365 (7.950%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` xenTro9 hg38) \
       > rbest.log 2>&1
    # real    749m24.229s

#############################################################################
# LASTZ human/hg38 vs. X. laevis/xenLae2 - (DONE - 2017-03-29 - Hiram)
    mkdir /hive/data/genomes/hg38/bed/lastzXenLae2.2017-03-29
    cd /hive/data/genomes/hg38/bed/lastzXenLae2.2017-03-29

    printf '# human vs X. laevis
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz
BLASTZ_O=400
BLASTZ_E=30
BLASTZ_Y=3400
BLASTZ_L=6000
BLASTZ_K=2200
BLASTZ_M=50
BLASTZ_Q=/scratch/data/blastz/HoxD55.q
#      A    C    G    T
#     91  -90  -25 -100
#    -90  100 -100  -25
#    -25 -100  100  -90
#   -100  -25  -90  91

# TARGET: human hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CTGDIR=/hive/data/genomes/hg38/hg38.contigs.2bit
SEQ1_CTGLEN=/hive/data/genomes/hg38/hg38.contigs.chrom.sizes
SEQ1_LIFT=/hive/data/genomes/hg38/jkStuff/hg38.contigs.lift
SEQ1_CHUNK=40000000
SEQ1_LIMIT=50
SEQ1_LAP=10000

# QUERY: X. laevis xenLae2
SEQ2_DIR=/hive/data/genomes/xenLae2/xenLae2.2bit
SEQ2_LEN=/hive/data/genomes/xenLae2/chrom.sizes
SEQ2_CHUNK=20000000
SEQ2_LIMIT=200
SEQ2_LAP=0

BASE=/hive/data/genomes/hg38/bed/lastzXenLae2.2017-03-29
TMPDIR=/dev/shm
' > DEF

    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
        -chainMinScore=5000 -chainLinearGap=loose \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > do.log 2>&1 &
    # real    952m1.703s

    cat fb.hg38.chainXenLae2Link.txt
    # 97526523 bases of 3049335806 (3.198%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` hg38 xenLae2) \
       > rbest.log 2>&1 &
    # real    650m25.803s

    # and for the swap:
    mkdir /hive/data/genomes/xenLae2/bed/blastz.hg38.swap
    cd /hive/data/genomes/xenLae2/bed/blastz.hg38.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/hg38/bed/lastzXenLae2.2017-03-29/DEF \
        -swap -chainMinScore=5000 -chainLinearGap=loose \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    #  real    28m54.570s

    cat fb.xenLae2.chainHg38Link.txt
    # 114726989 bases of 2408724787 (4.763%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` xenLae2 hg38) \
       > rbest.log 2>&1
    # real    712m34.326s

#########################################################################
# LASTZ human/hg38 vs. Chinese hamster CHO-K1 cell line/criGriChoV1
#	(DONE - 2017-04-13 - Hiram)

    mkdir /hive/data/genomes/hg38/bed/lastzCriGriChoV1.2017-04-13
    cd /hive/data/genomes/hg38/bed/lastzCriGriChoV1.2017-04-13

    printf '# human vs Chinese hamster ovary CHO-K1 cell line
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz
BLASTZ_M=254

# TARGET: human hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CTGDIR=/hive/data/genomes/hg38/hg38.contigs.2bit
SEQ1_CTGLEN=/hive/data/genomes/hg38/hg38.contigs.chrom.sizes
SEQ1_LIFT=/hive/data/genomes/hg38/jkStuff/hg38.contigs.lift
SEQ1_CHUNK=40000000
SEQ1_LIMIT=20
SEQ1_LAP=10000

# QUERY: Chinese hamster ovary CHO-K1 cell line criGriChoV1
SEQ2_DIR=/hive/data/genomes/criGriChoV1/criGriChoV1.2bit
SEQ2_LEN=/hive/data/genomes/criGriChoV1/chrom.sizes
SEQ2_CHUNK=20000000
SEQ2_LIMIT=200
SEQ2_LAP=0

BASE=/hive/data/genomes/hg38/bed/lastzCriGriChoV1.2017-04-13
TMPDIR=/dev/shm
' > DEF

    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
        -chainMinScore=3000 -chainLinearGap=medium \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -noDbNameCheck -syntenicNet) > do.log 2>&1
    # real    3327m39.074s

    cat fb.hg38.chainCriGriChoV1Link.txt
    # 973293331 bases of 3049335806 (31.918%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` hg38 criGriChoV1) \
       > rbest.log 2>&1 &
    # real    408m18.202s

    # and for the swap:
    mkdir /hive/data/genomes/criGriChoV1/bed/blastz.hg38.swap
    cd /hive/data/genomes/criGriChoV1/bed/blastz.hg38.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/hg38/bed/lastzCriGriChoV1.2017-04-13/DEF \
        -swap -chainMinScore=3000 -chainLinearGap=medium \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -noDbNameCheck -syntenicNet) > swap.log 2>&1
    #  real    91m19.847s

    cat fb.criGriChoV1.chainHg38Link.txt
    # 935724011 bases of 2318132242 (40.365%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` criGriChoV1 hg38) \
       > rbest.log 2>&1 &
    # real    436m55.979s

#########################################################################
# LASTZ human/hg38 Baboon/papAnu3 - (DONE - 2017-06-21 - Hiram)
    mkdir /hive/data/genomes/hg38/bed/lastzPapAnu3.2017-06-21
    cd /hive/data/genomes/hg38/bed/lastzPapAnu3.2017-06-21

    printf '# human vs baboon
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz
BLASTZ_M=254

# TARGET: human hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CTGDIR=/hive/data/genomes/hg38/hg38.contigs.2bit
SEQ1_CTGLEN=/hive/data/genomes/hg38/hg38.contigs.chrom.sizes
SEQ1_LIFT=/hive/data/genomes/hg38/jkStuff/hg38.contigs.lift
SEQ1_CHUNK=40000000
SEQ1_LIMIT=10
SEQ1_LAP=10000

# QUERY: Baboon papAnu3
SEQ2_DIR=/hive/data/genomes/papAnu3/papAnu3.2bit
SEQ2_LEN=/hive/data/genomes/papAnu3/chrom.sizes
SEQ2_CHUNK=20000000
SEQ2_LIMIT=150
SEQ2_LAP=0

BASE=/hive/data/genomes/hg38/bed/lastzPapAnu3.2017-06-21
TMPDIR=/dev/shm
' > DEF

    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
        -chainMinScore=3000 -chainLinearGap=medium \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > do.log 2>&1 &
    # real    1034m57.244s

    cat fb.hg38.chainPapAnu3Link.txt
    # 2632683317 bases of 3049335806 (86.336%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` hg38 papAnu3) \
        > rbest.log 2>&1 &
    # real    488m59.447s
    time (doRecipBest.pl -load -continue=load -workhorse=hgwdev \
	-buildDir=`pwd` hg38 papAnu3) > loadRBest.log 2>&1 &
    cat fb.hg38.chainRBestPapAnu3Link.txt
    # 2430072678 bases of 3049335806 (79.692%) in intersection

    # create and load up syntenic chainNet: 2017-10-27
cd /hive/data/genomes/hg38/bed/lastzPapAnu3.2017-06-21/axtChain
netToAxt hg38.papAnu3.syn.net.gz hg38.papAnu3.all.chain.gz \
/scratch/data/hg38/hg38.2bit /hive/data/genomes/papAnu3/papAnu3.2bit stdout \
  | axtSort stdin stdout \
     | axtToChain stdin /hive/data/genomes/hg38/chrom.sizes \
        /hive/data/genomes/papAnu3/chrom.sizes stdout \
            | gzip -c > hg38.papAnu3.syn.chain.gz
hgLoadChain -tIndex hg38 chainSynPapAnu3 hg38.papAnu3.syn.chain.gz
netFilter -minGap=10 hg38.papAnu3.syn.net.gz \
  | hgLoadNet -verbose=0 hg38 netSynPapAnu3 stdin
cd /hive/data/genomes/hg38/bed/lastzPapAnu3.2017-06-21
featureBits hg38 chainSynPapAnu3Link > fb.hg38.chainSynPapAnu3Link.txt 2>&1
cat fb.hg38.chainSynPapAnu3Link.txt
# 2570312354 bases of 3049335806 (84.291%) in intersection

    # and for the swap:
    mkdir /hive/data/genomes/papAnu3/bed/blastz.hg38.swap
    cd /hive/data/genomes/papAnu3/bed/blastz.hg38.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/hg38/bed/lastzPapAnu3.2017-06-21/DEF \
        -swap -chainMinScore=3000 -chainLinearGap=medium \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    #  real    232m5.391s

    cat fb.papAnu3.chainHg38Link.txt
    # 2501550280 bases of 2893270787 (86.461%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` papAnu3 hg38) \
      > rbest.log 2>&1
    # real    446m1.402s

#########################################################################
# LASTZ human/hg38 vs. pig/susScr11 - (DONE - 2017-07-31 - Hiram)
    mkdir /hive/data/genomes/hg38/bed/lastzSusScr11.2017-07-31
    cd /hive/data/genomes/hg38/bed/lastzSusScr11.2017-07-31

    printf '# human vs pig
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz
BLASTZ_O=400
BLASTZ_E=30
BLASTZ_M=254
# default BLASTZ_Q score matrix:
#       A     C     G     T
# A    91  -114   -31  -123
# C  -114   100  -125   -31
# G   -31  -125   100  -114
# T  -123   -31  -114    91

# TARGET: human hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CTGDIR=/hive/data/genomes/hg38/hg38.contigs.2bit
SEQ1_CTGLEN=/hive/data/genomes/hg38/hg38.contigs.chrom.sizes
SEQ1_LIFT=/hive/data/genomes/hg38/jkStuff/hg38.contigs.lift
SEQ1_CHUNK=40000000
SEQ1_LIMIT=5
SEQ1_LAP=10000

# QUERY: pig susScr11
SEQ2_DIR=/hive/data/genomes/susScr11/susScr11.2bit
SEQ2_LEN=/hive/data/genomes/susScr11/chrom.sizes
SEQ2_CHUNK=20000000
SEQ2_LIMIT=5
SEQ2_LAP=0

BASE=/hive/data/genomes/hg38/bed/lastzSusScr11.2017-07-31
TMPDIR=/dev/shm
'> DEF

    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
        -chainMinScore=3000 -chainLinearGap=medium \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > do.log 2>&1
    # real    638m46.019s

    cat fb.hg38.chainSusScr11Link.txt
    # 1463754915 bases of 3049335806 (48.002%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` hg38 susScr11) \
	> rbest.log 2>&1 &
    # real    664m31.094s

    # and for the swap:
    mkdir /hive/data/genomes/susScr11/bed/blastz.hg38.swap
    cd /hive/data/genomes/susScr11/bed/blastz.hg38.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/hg38/bed/lastzSusScr11.2017-07-31/DEF \
        -swap -chainMinScore=3000 -chainLinearGap=medium \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    #  real    107m7.364s

    cat fb.susScr11.chainHg38Link.txt
    # 1387973267 bases of 2472073034 (56.146%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` susScr11 hg38) \
        > rbest.log 2>&1
    # real    598m8.675s

#########################################################################
# LASTZ human/hg38 vs. Nile tilapia/oreNil3 - (DONE - 2017-07-31 - Hiram)
    mkdir /hive/data/genomes/hg38/bed/lastzOreNil3.2017-07-31
    cd /hive/data/genomes/hg38/bed/lastzOreNil3.2017-07-31

    printf '# human vs Nile tilapia
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz
BLASTZ_O=400
BLASTZ_E=30
BLASTZ_Y=3400
BLASTZ_L=6000
BLASTZ_K=2200
BLASTZ_M=50
BLASTZ_Q=/scratch/data/blastz/HoxD55.q
#      A    C    G    T
#     91  -90  -25 -100
#    -90  100 -100  -25
#    -25 -100  100  -90
#   -100  -25  -90  91

# TARGET: human hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CTGDIR=/hive/data/genomes/hg38/hg38.contigs.2bit
SEQ1_CTGLEN=/hive/data/genomes/hg38/hg38.contigs.chrom.sizes
SEQ1_LIFT=/hive/data/genomes/hg38/jkStuff/hg38.contigs.lift
SEQ1_CHUNK=40000000
SEQ1_LIMIT=5
SEQ1_LAP=10000

# QUERY: Nile tilapia oreNil3
SEQ2_DIR=/hive/data/genomes/oreNil3/oreNil3.2bit
SEQ2_LEN=/hive/data/genomes/oreNil3/chrom.sizes
SEQ2_CHUNK=20000000
SEQ2_LIMIT=10
SEQ2_LAP=0

BASE=/hive/data/genomes/hg38/bed/lastzOreNil3.2017-07-31
TMPDIR=/dev/shm
' > DEF

    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
        -chainMinScore=5000 -chainLinearGap=loose \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > do.log 2>&1 &
    # real    318m42.840s

    cat fb.hg38.chainOreNil3Link.txt
    # 59963651 bases of 3049335806 (1.966%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` hg38 oreNil3) \
       > rbest.log 2>&1 &
    # real    275m9.491s

    # and for the swap:
    mkdir /hive/data/genomes/oreNil3/bed/blastz.hg38.swap
    cd /hive/data/genomes/oreNil3/bed/blastz.hg38.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/hg38/bed/lastzOreNil3.2017-07-31/DEF \
        -swap -chainMinScore=5000 -chainLinearGap=loose \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    #  real    8m59.810s

    cat fb.oreNil3.chainHg38Link.txt
    # 56298016 bases of 1009856516 (5.575%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` oreNil3 hg38) \
       > rbest.log 2>&1
    # real    263m17.904s

#########################################################################
# LASTZ human/hg38 drill/manLeu1 - (DONE - 2017-09-25 - Hiram)
    mkdir /hive/data/genomes/hg38/bed/lastzManLeu1.2017-09-25
    cd /hive/data/genomes/hg38/bed/lastzManLeu1.2017-09-25

    printf '# human vs drill
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz
# maximum M allowed with lastz is only 254
BLASTZ_M=254
BLASTZ_Q=/scratch/data/blastz/human_chimp.v2.q
BLASTZ_O=600
BLASTZ_E=150
# other parameters from panTro2 vs hg18 lastz on advice from Webb
BLASTZ_K=4500
BLASTZ_Y=15000
BLASTZ_T=2

# TARGET: Human Hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CTGDIR=/hive/data/genomes/hg38/hg38.contigs.2bit
SEQ1_CTGLEN=/hive/data/genomes/hg38/hg38.contigs.chrom.sizes
SEQ1_LIFT=/hive/data/genomes/hg38/jkStuff/hg38.contigs.lift
SEQ1_CHUNK=20000000
SEQ1_LAP=10000

# QUERY: Drill/Mandrillus leucophaeus manLeu1
SEQ2_DIR=/hive/data/genomes/manLeu1/manLeu1.2bit
SEQ2_LEN=/hive/data/genomes/manLeu1/chrom.sizes
SEQ2_CHUNK=20000000
SEQ2_LIMIT=40
SEQ2_LAP=0
SEQ2_IN_CONTIGS=0

BASE=/hive/data/genomes/hg38/bed/lastzManLeu1.2017-09-25
TMPDIR=/dev/shm
' > DEF
    # << happy emacs

    time (doBlastzChainNet.pl -verbose=2 `pwd`/DEF \
        -syntenicNet -fileServer=hgwdev \
        -chainMinScore=5000 -chainLinearGap=medium \
        -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku) > do.log 2>&1
    # real    121m0.485s

    cat fb.hg38.chainManLeu1Link.txt
    # 2515634714 bases of 3049335806 (82.498%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` hg38 manLeu1) \
	> rbest.log 2>&1 &
    # real    287m28.553s
    time (doRecipBest.pl -load -continue=load -workhorse=hgwdev \
	-buildDir=`pwd` hg38 manLeu1) > loadRBest.log 2>&1 &
    cat fb.hg38.chainRBestManLeu1Link.txt
    # 2346062769 bases of 3049335806 (76.937%) in intersection

    # create and load up syntenic chainNet: 2017-10-27
cd /hive/data/genomes/hg38/bed/lastzManLeu1.2017-09-25/axtChain
netToAxt hg38.manLeu1.syn.net.gz hg38.manLeu1.all.chain.gz \
/scratch/data/hg38/hg38.2bit /hive/data/genomes/manLeu1/manLeu1.2bit stdout \
  | axtSort stdin stdout \
     | axtToChain stdin /hive/data/genomes/hg38/chrom.sizes \
        /hive/data/genomes/manLeu1/chrom.sizes stdout \
            | gzip -c > hg38.manLeu1.syn.chain.gz
hgLoadChain -tIndex hg38 chainSynManLeu1 hg38.manLeu1.syn.chain.gz
netFilter -minGap=10 hg38.manLeu1.syn.net.gz \
  | hgLoadNet -verbose=0 hg38 netSynManLeu1 stdin
cd /hive/data/genomes/hg38/bed/lastzManLeu1.2017-09-25
featureBits hg38 chainSynManLeu1Link > fb.hg38.chainSynManLeu1Link.txt 2>&1
cat fb.hg38.chainSynManLeu1Link.txt
# 2472880015 bases of 3049335806 (81.096%) in intersection

    # and for the swap:
    mkdir /hive/data/genomes/manLeu1/bed/blastz.hg38.swap
    cd /hive/data/genomes/manLeu1/bed/blastz.hg38.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/hg38/bed/lastzManLeu1.2017-09-25/DEF \
        -swap -chainMinScore=5000 -chainLinearGap=medium \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    #  real    79m34.951s

    cat fb.manLeu1.chainHg38Link.txt
    # 2409820927 bases of 2721424086 (88.550%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` manLeu1 hg38) \
	> rbest.log 2>&1
    # real    388m23.086s

#########################################################################
# LASTZ human/hg38 vs. Ma's night monkey/aotNan1 - (DONE - 2017-09-25 - Hiram)
    mkdir /hive/data/genomes/hg38/bed/lastzAotNan1.2017-09-25
    cd /hive/data/genomes/hg38/bed/lastzAotNan1.2017-09-25

    printf '# human vs Ma_s night monkey
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz
# maximum M allowed with lastz is only 254
BLASTZ_M=254
BLASTZ_Q=/scratch/data/blastz/human_chimp.v2.q
BLASTZ_O=600
BLASTZ_E=150
# other parameters from panTro2 vs hg18 lastz on advice from Webb
BLASTZ_K=4500
BLASTZ_Y=15000
BLASTZ_T=2

# TARGET: Human Hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CTGDIR=/hive/data/genomes/hg38/hg38.contigs.2bit
SEQ1_CTGLEN=/hive/data/genomes/hg38/hg38.contigs.chrom.sizes
SEQ1_LIFT=/hive/data/genomes/hg38/jkStuff/hg38.contigs.lift
SEQ1_CHUNK=20000000
SEQ1_LAP=10000

# QUERY: aotNan1 - Ma_s night monkey - Aotus nancymaae
SEQ2_DIR=/hive/data/genomes/aotNan1/aotNan1.2bit
SEQ2_LEN=/hive/data/genomes/aotNan1/chrom.sizes
SEQ2_CHUNK=20000000
SEQ2_LIMIT=100
SEQ2_LAP=0
SEQ2_IN_CONTIGS=0

BASE=/hive/data/genomes/hg38/bed/lastzAotNan1.2017-09-25
TMPDIR=/dev/shm
' > DEF
    # << happy emacs

    time (doBlastzChainNet.pl -verbose=2 `pwd`/DEF \
        -syntenicNet -fileServer=hgwdev \
        -chainMinScore=5000 -chainLinearGap=medium \
        -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku) > do.log 2>&1
    # real    205m4.426s

    cat fb.hg38.chainAotNan1Link.txt
    # 2153726630 bases of 3049335806 (70.629%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` hg38 aotNan1) \
	> rbest.log 2>&1 &
    # real    269m4.216s
    time (doRecipBest.pl -load -continue=load -workhorse=hgwdev \
	-buildDir=`pwd` hg38 aotNan1) > loadRBest.log 2>&1 &
    cat fb.hg38.chainRBestAotNan1Link.txt
    # 2013684675 bases of 3049335806 (66.037%) in intersection

    # create and load up syntenic chainNet: 2017-10-27
cd /hive/data/genomes/hg38/bed/lastzAotNan1.2017-09-25/axtChain
netToAxt hg38.aotNan1.syn.net.gz hg38.aotNan1.all.chain.gz \
/scratch/data/hg38/hg38.2bit /hive/data/genomes/aotNan1/aotNan1.2bit stdout \
  | axtSort stdin stdout \
     | axtToChain stdin /hive/data/genomes/hg38/chrom.sizes \
        /hive/data/genomes/aotNan1/chrom.sizes stdout \
            | gzip -c > hg38.aotNan1.syn.chain.gz
hgLoadChain -tIndex hg38 chainSynAotNan1 hg38.aotNan1.syn.chain.gz
netFilter -minGap=10 hg38.aotNan1.syn.net.gz \
  | hgLoadNet -verbose=0 hg38 netSynAotNan1 stdin
cd /hive/data/genomes/hg38/bed/lastzAotNan1.2017-09-25
featureBits hg38 chainSynAotNan1Link > fb.hg38.chainSynAotNan1Link.txt 2>&1
cat fb.hg38.chainSynAotNan1Link.txt
# 2098197465 bases of 3049335806 (68.808%) in intersection

    # and for the swap:
    mkdir /hive/data/genomes/aotNan1/bed/blastz.hg38.swap
    cd /hive/data/genomes/aotNan1/bed/blastz.hg38.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/hg38/bed/lastzAotNan1.2017-09-25/DEF \
        -swap -chainMinScore=5000 -chainLinearGap=medium \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    #  real    84m8.440s

    cat fb.aotNan1.chainHg38Link.txt
    # 2111600029 bases of 2714439490 (77.791%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` aotNan1 hg38) \
	> rbest.log 2>&1
    # real    427m26.453s

#########################################################################
# LASTZ human/hg38 vs. Hawaiian monk seal/neoSch1 - (DONE - 2017-09-25 - Hiram)
    mkdir /hive/data/genomes/hg38/bed/lastzNeoSch1.2017-09-25
    cd /hive/data/genomes/hg38/bed/lastzNeoSch1.2017-09-25

    printf '# human vs Hawaiian monk seal
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz
BLASTZ_O=400
BLASTZ_E=30
BLASTZ_M=254
# default BLASTZ_Q score matrix:
#       A     C     G     T
# A    91  -114   -31  -123
# C  -114   100  -125   -31
# G   -31  -125   100  -114
# T  -123   -31  -114    91

# TARGET: human hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CTGDIR=/hive/data/genomes/hg38/hg38.contigs.2bit
SEQ1_CTGLEN=/hive/data/genomes/hg38/hg38.contigs.chrom.sizes
SEQ1_LIFT=/hive/data/genomes/hg38/jkStuff/hg38.contigs.lift
SEQ1_CHUNK=40000000
SEQ1_LIMIT=5
SEQ1_LAP=10000

# QUERY: Hawaiian monk seal - neoSch1
SEQ2_DIR=/hive/data/genomes/neoSch1/neoSch1.2bit
SEQ2_LEN=/hive/data/genomes/neoSch1/chrom.sizes
SEQ2_CHUNK=20000000
SEQ2_LIMIT=50
SEQ2_LAP=0

BASE=/hive/data/genomes/hg38/bed/lastzNeoSch1.2017-09-25
TMPDIR=/dev/shm
'> DEF

    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
        -chainMinScore=3000 -chainLinearGap=medium \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > do.log 2>&1
    # real    512m6.939s

    cat fb.hg38.chainNeoSch1Link.txt
    # 1586260720 bases of 3049335806 (52.020%) in intersection
    cat fb.hg38.chainSynNeoSch1Link.txt
    # 1515015853 bases of 3049335806 (49.683%) in intersection

    time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` hg38 neoSch1) \
	> rbest.log 2>&1 &
    # real    475m3.278s

    cat fb.hg38.chainRBestNeoSch1Link.txt
    # 1455520429 bases of 3049335806 (47.732%) in intersection

    # and for the swap:
    mkdir /hive/data/genomes/neoSch1/bed/blastz.hg38.swap
    cd /hive/data/genomes/neoSch1/bed/blastz.hg38.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/hg38/bed/lastzNeoSch1.2017-09-25/DEF \
        -swap -chainMinScore=3000 -chainLinearGap=medium \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    #  real    108m21.523s

    cat fb.neoSch1.chainHg38Link.txt
    # 1483929997 bases of 2400839308 (61.809%) in intersection
    cat fb.neoSch1.chainSynHg38Link.txt
    # 1446564285 bases of 2400839308 (60.252%) in intersection

    time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` neoSch1 hg38) \
        > rbest.log 2>&1
    # real    404m14.530s

    cat fb.neoSch1.chainRBestHg38Link.txt
    # 1455431042 bases of 2400839308 (60.622%) in intersection

#########################################################################
# LASTZ human/hg38 vs. Sooty mangabey/cerAty1 - (DONE - 2017-09-27 - Hiram)
    mkdir /hive/data/genomes/hg38/bed/lastzCerAty1.2017-09-27
    cd /hive/data/genomes/hg38/bed/lastzCerAty1.2017-09-27

    printf '# human vs Sooty mangabey
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz
# maximum M allowed with lastz is only 254
BLASTZ_M=254
BLASTZ_Q=/scratch/data/blastz/human_chimp.v2.q
BLASTZ_O=600
BLASTZ_E=150
# other parameters from panTro2 vs hg18 lastz on advice from Webb
BLASTZ_K=4500
BLASTZ_Y=15000
BLASTZ_T=2

# TARGET: Human Hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CTGDIR=/hive/data/genomes/hg38/hg38.contigs.2bit
SEQ1_CTGLEN=/hive/data/genomes/hg38/hg38.contigs.chrom.sizes
SEQ1_LIFT=/hive/data/genomes/hg38/jkStuff/hg38.contigs.lift
SEQ1_CHUNK=20000000
SEQ1_LAP=10000

# QUERY: cerAty1 - Sooty mangabey - Cercocebus atys
SEQ2_DIR=/hive/data/genomes/cerAty1/cerAty1.2bit
SEQ2_LEN=/hive/data/genomes/cerAty1/chrom.sizes
SEQ2_CHUNK=20000000
SEQ2_LIMIT=50
SEQ2_LAP=0
SEQ2_IN_CONTIGS=0

BASE=/hive/data/genomes/hg38/bed/lastzCerAty1.2017-09-27
TMPDIR=/dev/shm
' > DEF

    time (doBlastzChainNet.pl -verbose=2 `pwd`/DEF \
        -syntenicNet -fileServer=hgwdev \
        -chainMinScore=5000 -chainLinearGap=medium \
        -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku) > do.log 2>&1
    # real    202m34.990s

    cat fb.hg38.chainCerAty1Link.txt
    # 2556764791 bases of 3049335806 (83.847%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` hg38 cerAty1) \
	> rbest.log 2>&1 &
    # real    188m38.348s
    time (doRecipBest.pl -load -continue=load -workhorse=hgwdev \
	-buildDir=`pwd` hg38 cerAty1) > loadRBest.log 2>&1 &
    cat fb.hg38.chainRBestCerAty1Link.txt
    # 2383692825 bases of 3049335806 (78.171%) in intersection

    # create and load up syntenic chainNet: 2017-10-27
cd /hive/data/genomes/hg38/bed/lastzCerAty1.2017-09-27/axtChain
netToAxt hg38.cerAty1.syn.net.gz hg38.cerAty1.all.chain.gz \
/scratch/data/hg38/hg38.2bit /hive/data/genomes/cerAty1/cerAty1.2bit stdout \
  | axtSort stdin stdout \
     | axtToChain stdin /hive/data/genomes/hg38/chrom.sizes \
        /hive/data/genomes/cerAty1/chrom.sizes stdout \
            | gzip -c > hg38.cerAty1.syn.chain.gz
hgLoadChain -tIndex hg38 chainSynCerAty1 hg38.cerAty1.syn.chain.gz
netFilter -minGap=10 hg38.cerAty1.syn.net.gz \
  | hgLoadNet -verbose=0 hg38 netSynCerAty1 stdin
cd /hive/data/genomes/hg38/bed/lastzCerAty1.2017-09-27
featureBits hg38 chainSynCerAty1Link > fb.hg38.chainSynCerAty1Link.txt 2>&1
cat fb.hg38.chainSynCerAty1Link.txt
# 2516680168 bases of 3049335806 (82.532%) in intersection

    # and for the swap:
    mkdir /hive/data/genomes/cerAty1/bed/blastz.hg38.swap
    cd /hive/data/genomes/cerAty1/bed/blastz.hg38.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/hg38/bed/lastzCerAty1.2017-09-27/DEF \
        -swap -chainMinScore=5000 -chainLinearGap=medium \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    #  real    84m53.559s

    cat fb.cerAty1.chainHg38Link.txt
    # 2424226994 bases of 2787289397 (86.974%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` cerAty1 hg38) \
	> rbest.log 2>&1
    # real    226m2.420s

#########################################################################
# LASTZ human/hg38 vs. Sooty mangabey/proCoq1 - (DONE - 2017-09-28 - Hiram)
    mkdir /hive/data/genomes/hg38/bed/lastzProCoq1.2017-09-28
    cd /hive/data/genomes/hg38/bed/lastzProCoq1.2017-09-28

    printf '# human vs Coquerel_s sifaka
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz
# maximum M allowed with lastz is only 254
BLASTZ_M=254
BLASTZ_Q=/scratch/data/blastz/human_chimp.v2.q
BLASTZ_O=600
BLASTZ_E=150
# other parameters from panTro2 vs hg18 lastz on advice from Webb
BLASTZ_K=4500
BLASTZ_Y=15000
BLASTZ_T=2

# TARGET: Human Hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CTGDIR=/hive/data/genomes/hg38/hg38.contigs.2bit
SEQ1_CTGLEN=/hive/data/genomes/hg38/hg38.contigs.chrom.sizes
SEQ1_LIFT=/hive/data/genomes/hg38/jkStuff/hg38.contigs.lift
SEQ1_CHUNK=20000000
SEQ1_LAP=10000

# QUERY: proCoq1 - Coquerel_s sifaka - Propithecus coquereli
SEQ2_DIR=/hive/data/genomes/proCoq1/proCoq1.2bit
SEQ2_LEN=/hive/data/genomes/proCoq1/chrom.sizes
SEQ2_CHUNK=20000000
SEQ2_LIMIT=70
SEQ2_LAP=0
SEQ2_IN_CONTIGS=0

BASE=/hive/data/genomes/hg38/bed/lastzProCoq1.2017-09-28
TMPDIR=/dev/shm
' > DEF

    time (doBlastzChainNet.pl -verbose=2 `pwd`/DEF \
        -syntenicNet -fileServer=hgwdev \
        -chainMinScore=5000 -chainLinearGap=medium \
        -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku) > do.log 2>&1
    # real    110m38.813s

    cat fb.hg38.chainProCoq1Link.txt
    # 990017370 bases of 3049335806 (32.467%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` hg38 proCoq1) \
	> rbest.log 2>&1 &
    # real    330m51.520s
    time (doRecipBest.pl -load -continue=load -workhorse=hgwdev \
	-buildDir=`pwd` hg38 proCoq1) > rbest.log 2>&1 &
    cat fb.hg38.chainRBestProCoq1Link.txt
    # 935801596 bases of 3049335806 (30.689%) in intersection

    # create and load up syntenic chainNet: 2017-10-27
cd /hive/data/genomes/hg38/bed/lastzProCoq1.2017-09-28/axtChain
netToAxt hg38.proCoq1.syn.net.gz hg38.proCoq1.all.chain.gz \
/scratch/data/hg38/hg38.2bit /hive/data/genomes/proCoq1/proCoq1.2bit stdout \
  | axtSort stdin stdout \
     | axtToChain stdin /hive/data/genomes/hg38/chrom.sizes \
        /hive/data/genomes/proCoq1/chrom.sizes stdout \
            | gzip -c > hg38.proCoq1.syn.chain.gz
hgLoadChain -tIndex hg38 chainSynProCoq1 hg38.proCoq1.syn.chain.gz
netFilter -minGap=10 hg38.proCoq1.syn.net.gz \
  | hgLoadNet -verbose=0 hg38 netSynProCoq1 stdin
cd /hive/data/genomes/hg38/bed/lastzProCoq1.2017-09-28
featureBits hg38 chainSynProCoq1Link > fb.hg38.chainSynProCoq1Link.txt 2>&1
cat fb.hg38.chainSynProCoq1Link.txt
# 943897639 bases of 3049335806 (30.954%) in intersection

    # and for the swap:
    mkdir /hive/data/genomes/proCoq1/bed/blastz.hg38.swap
    cd /hive/data/genomes/proCoq1/bed/blastz.hg38.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/hg38/bed/lastzProCoq1.2017-09-28/DEF \
        -swap -chainMinScore=5000 -chainLinearGap=medium \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    #  real    44m29.295s

    cat fb.proCoq1.chainHg38Link.txt
    # 953092997 bases of 2083764538 (45.739%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` proCoq1 hg38) \
	> rbest.log 2>&1
    # real    334m45.550s

#########################################################################
# LASTZ human/hg38 vs. White-faced sapajou/cebCap1 - (DONE - 2017-09-28 - Hiram)
    mkdir /hive/data/genomes/hg38/bed/lastzCebCap1.2017-09-28
    cd /hive/data/genomes/hg38/bed/lastzCebCap1.2017-09-28

    printf '# human vs White-faced sapajou
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz
# maximum M allowed with lastz is only 254
BLASTZ_M=254
BLASTZ_Q=/scratch/data/blastz/human_chimp.v2.q
BLASTZ_O=600
BLASTZ_E=150
# other parameters from panTro2 vs hg18 lastz on advice from Webb
BLASTZ_K=4500
BLASTZ_Y=15000
BLASTZ_T=2

# TARGET: Human Hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CTGDIR=/hive/data/genomes/hg38/hg38.contigs.2bit
SEQ1_CTGLEN=/hive/data/genomes/hg38/hg38.contigs.chrom.sizes
SEQ1_LIFT=/hive/data/genomes/hg38/jkStuff/hg38.contigs.lift
SEQ1_CHUNK=20000000
SEQ1_LAP=10000

# QUERY: cebCap1 - White-faced sapajou -  Cebus capucinus imitator
SEQ2_DIR=/hive/data/genomes/cebCap1/cebCap1.2bit
SEQ2_LEN=/hive/data/genomes/cebCap1/chrom.sizes
SEQ2_CHUNK=20000000
SEQ2_LIMIT=30
SEQ2_LAP=0
SEQ2_IN_CONTIGS=0

BASE=/hive/data/genomes/hg38/bed/lastzCebCap1.2017-09-28
TMPDIR=/dev/shm
' > DEF

    time (doBlastzChainNet.pl -verbose=2 `pwd`/DEF \
        -syntenicNet -fileServer=hgwdev \
        -chainMinScore=5000 -chainLinearGap=medium \
        -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku) > do.log 2>&1
    # real    169m20.421s

    cat fb.hg38.chainCebCap1Link.txt
    # 2155370668 bases of 3049335806 (70.683%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` hg38 cebCap1) \
	> rbest.log 2>&1 &
    # real    210m50.610s
    time (doRecipBest.pl -load -continue=load -workhorse=hgwdev \
	-buildDir=`pwd` hg38 cebCap1) > loadRBest.log 2>&1 &
    cat fb.hg38.chainRBestCebCap1Link.txt
    # 2011508311 bases of 3049335806 (65.965%) in intersection

    # create and load up syntenic chainNet: 2017-10-27
cd /hive/data/genomes/hg38/bed/lastzCebCap1.2017-09-28/axtChain
netToAxt hg38.cebCap1.syn.net.gz hg38.cebCap1.all.chain.gz \
/scratch/data/hg38/hg38.2bit /hive/data/genomes/cebCap1/cebCap1.2bit stdout \
  | axtSort stdin stdout \
     | axtToChain stdin /hive/data/genomes/hg38/chrom.sizes \
        /hive/data/genomes/cebCap1/chrom.sizes stdout \
            | gzip -c > hg38.cebCap1.syn.chain.gz
hgLoadChain -tIndex hg38 chainSynCebCap1 hg38.cebCap1.syn.chain.gz
netFilter -minGap=10 hg38.cebCap1.syn.net.gz \
  | hgLoadNet -verbose=0 hg38 netSynCebCap1 stdin
cd /hive/data/genomes/hg38/bed/lastzCebCap1.2017-09-28
featureBits hg38 chainSynCebCap1Link > fb.hg38.chainSynCebCap1Link.txt 2>&1
cat fb.hg38.chainSynCebCap1Link.txt
# 2113665551 bases of 3049335806 (69.316%) in intersection

    # and for the swap:
    mkdir /hive/data/genomes/cebCap1/bed/blastz.hg38.swap
    cd /hive/data/genomes/cebCap1/bed/blastz.hg38.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/hg38/bed/lastzCebCap1.2017-09-28/DEF \
        -swap -chainMinScore=5000 -chainLinearGap=medium \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    #  real    76m58.704s

    cat fb.cebCap1.chainHg38Link.txt
    # 2053319068 bases of 2610518382 (78.656%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` cebCap1 hg38) \
	> rbest.log 2>&1
    # real    227m7.064s

#########################################################################
# LASTZ human/hg38 vs. Sclater's lemur/eulFla1 - (DONE - 2017-10-03 - Hiram)
    mkdir /hive/data/genomes/hg38/bed/lastzEulFla1.2017-10-03
    cd /hive/data/genomes/hg38/bed/lastzEulFla1.2017-10-03

    printf '# human vs Sclater_s lemur
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz
# maximum M allowed with lastz is only 254
BLASTZ_M=254
BLASTZ_Q=/scratch/data/blastz/human_chimp.v2.q
BLASTZ_O=600
BLASTZ_E=150
# other parameters from panTro2 vs hg18 lastz on advice from Webb
BLASTZ_K=4500
BLASTZ_Y=15000
BLASTZ_T=2

# TARGET: Human Hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CTGDIR=/hive/data/genomes/hg38/hg38.contigs.2bit
SEQ1_CTGLEN=/hive/data/genomes/hg38/hg38.contigs.chrom.sizes
SEQ1_LIFT=/hive/data/genomes/hg38/jkStuff/hg38.contigs.lift
SEQ1_CHUNK=20000000
SEQ1_LAP=10000

# QUERY: eulFla1 - Sclater_s lemur - Eulemur flavifrons
SEQ2_DIR=/hive/data/genomes/eulFla1/eulFla1.2bit
SEQ2_LEN=/hive/data/genomes/eulFla1/chrom.sizes
SEQ2_CHUNK=20000000
SEQ2_LIMIT=100
SEQ2_LAP=0
SEQ2_IN_CONTIGS=0

BASE=/hive/data/genomes/hg38/bed/lastzEulFla1.2017-10-03
TMPDIR=/dev/shm
' > DEF

    time (doBlastzChainNet.pl -verbose=2 `pwd`/DEF \
        -syntenicNet -fileServer=hgwdev \
        -chainMinScore=5000 -chainLinearGap=medium \
        -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku) > do.log 2>&1
    # real    130m37.028s

    cat fb.hg38.chainEulFla1Link.txt
    # 1016209837 bases of 3049335806 (33.326%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` hg38 eulFla1) \
	> rbest.log 2>&1 &
    # real    214m11.636s
    # loading the recip best results
    time (doRecipBest.pl -load -continue=load -workhorse=hgwdev -buildDir=`pwd` hg38 eulFla1) \
	> loadRBest.log 2>&1 &
    # real    5m38.039s
    cat fb.hg38.chainRBestEulFla1Link.txt
    # 961423111 bases of 3049335806 (31.529%) in intersection

    # create and load up syntenic chainNet: 2017-10-27
cd /hive/data/genomes/hg38/bed/lastzEulFla1.2017-10-03/axtChain
netToAxt hg38.eulFla1.syn.net.gz hg38.eulFla1.all.chain.gz \
/scratch/data/hg38/hg38.2bit /hive/data/genomes/eulFla1/eulFla1.2bit stdout \
  | axtSort stdin stdout \
     | axtToChain stdin /hive/data/genomes/hg38/chrom.sizes \
        /hive/data/genomes/eulFla1/chrom.sizes stdout \
            | gzip -c > hg38.eulFla1.syn.chain.gz
hgLoadChain -tIndex hg38 chainSynEulFla1 hg38.eulFla1.syn.chain.gz
netFilter -minGap=10 hg38.eulFla1.syn.net.gz \
  | hgLoadNet -verbose=0 hg38 netSynEulFla1 stdin
cd /hive/data/genomes/hg38/bed/lastzEulFla1.2017-10-03
featureBits hg38 chainSynEulFla1Link > fb.hg38.chainSynEulFla1Link.txt 2>&1
    # real    7m20.440s

cat fb.hg38.chainSynEulFla1Link.txt
    # 973484798 bases of 3049335806 (31.924%) in intersection

    # and for the swap:
    mkdir /hive/data/genomes/eulFla1/bed/blastz.hg38.swap
    cd /hive/data/genomes/eulFla1/bed/blastz.hg38.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/hg38/bed/lastzEulFla1.2017-10-03/DEF \
        -swap -chainMinScore=5000 -chainLinearGap=medium \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    #  real    48m20.179s

    cat fb.eulFla1.chainHg38Link.txt
    # 969761746 bases of 2094103399 (46.309%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` eulFla1 hg38) \
	> rbest.log 2>&1
    # real    199m39.734s
    time ($HOME/kent/src/hg/utils/automation/doRecipBest.pl -load -continue=load -workhorse=hgwdev -buildDir=`pwd` eulFla1 hg38) \
	> loadRBest.log 2>&1
    # real    6m23.578s
    cat fb.eulFla1.chainRBestHg38Link.txt
    # 961226273 bases of 2094103399 (45.902%) in intersection

#########################################################################
# LASTZ human/hg38 vs. Black lemur/eulMac1 - (DONE - 2017-10-04 - Hiram)
    mkdir /hive/data/genomes/hg38/bed/lastzEulMac1.2017-10-04
    cd /hive/data/genomes/hg38/bed/lastzEulMac1.2017-10-04

    printf '# human vs Black lemur
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz
# maximum M allowed with lastz is only 254
BLASTZ_M=254
BLASTZ_Q=/scratch/data/blastz/human_chimp.v2.q
BLASTZ_O=600
BLASTZ_E=150
# other parameters from panTro2 vs hg18 lastz on advice from Webb
BLASTZ_K=4500
BLASTZ_Y=15000
BLASTZ_T=2

# TARGET: Human Hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CTGDIR=/hive/data/genomes/hg38/hg38.contigs.2bit
SEQ1_CTGLEN=/hive/data/genomes/hg38/hg38.contigs.chrom.sizes
SEQ1_LIFT=/hive/data/genomes/hg38/jkStuff/hg38.contigs.lift
SEQ1_CHUNK=20000000
SEQ1_LAP=10000

# QUERY: eulMac1 - Black lemur - Eulemur macaco
SEQ2_DIR=/hive/data/genomes/eulMac1/eulMac1.2bit
SEQ2_LEN=/hive/data/genomes/eulMac1/chrom.sizes
SEQ2_CHUNK=20000000
SEQ2_LIMIT=100
SEQ2_LAP=0
SEQ2_IN_CONTIGS=0

BASE=/hive/data/genomes/hg38/bed/lastzEulMac1.2017-10-04
TMPDIR=/dev/shm
' > DEF

    time (doBlastzChainNet.pl -verbose=2 `pwd`/DEF \
        -syntenicNet -fileServer=hgwdev \
        -chainMinScore=5000 -chainLinearGap=medium \
        -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku) > do.log 2>&1
    # real    66m41.057s

    cat fb.hg38.chainEulMac1Link.txt
    # 1027856175 bases of 3049335806 (33.708%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` hg38 eulMac1) \
	> rbest.log 2>&1 &
    # real    220m20.185s
    time (doRecipBest.pl -load -continue=load -workhorse=hgwdev \
	-buildDir=`pwd` hg38 eulMac1) > rbest.log 2>&1 &
    # real    6m20.657s

    cat fb.hg38.chainRBestEulMac1Link.txt
    972709793 bases of 3049335806 (31.899%) in intersection

    # create and load up syntenic chainNet: 2017-10-27
cd /hive/data/genomes/hg38/bed/lastzEulMac1.2017-10-04/axtChain
netToAxt hg38.eulMac1.syn.net.gz hg38.eulMac1.all.chain.gz \
/scratch/data/hg38/hg38.2bit /hive/data/genomes/eulMac1/eulMac1.2bit stdout \
  | axtSort stdin stdout \
     | axtToChain stdin /hive/data/genomes/hg38/chrom.sizes \
        /hive/data/genomes/eulMac1/chrom.sizes stdout \
            | gzip -c > hg38.eulMac1.syn.chain.gz
hgLoadChain -tIndex hg38 chainSynEulMac1 hg38.eulMac1.syn.chain.gz
netFilter -minGap=10 hg38.eulMac1.syn.net.gz \
  | hgLoadNet -verbose=0 hg38 netSynEulMac1 stdin
cd /hive/data/genomes/hg38/bed/lastzEulMac1.2017-10-04
featureBits hg38 chainSynEulMac1Link > fb.hg38.chainSynEulMac1Link.txt 2>&1
cat fb.hg38.chainSynEulMac1Link.txt
# 983839076 bases of 3049335806 (32.264%) in intersection

    # and for the swap:
    mkdir /hive/data/genomes/eulMac1/bed/blastz.hg38.swap
    cd /hive/data/genomes/eulMac1/bed/blastz.hg38.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/hg38/bed/lastzEulMac1.2017-10-04/DEF \
        -swap -chainMinScore=5000 -chainLinearGap=medium \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    #  real    47m2.650s

    cat fb.eulMac1.chainHg38Link.txt
    # 979925982 bases of 2101039320 (46.640%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` eulMac1 hg38) \
	> rbest.log 2>&1
    # real    200m34.710s

#########################################################################
# LASTZ Human/hg38 - Tarsier TarSyr2 (DONE - 2014-12-11 - Hiram)
    mkdir /hive/data/genomes/hg38/bed/lastzTarSyr2.2014-12-11
    cd /hive/data/genomes/hg38/bed/lastzTarSyr2.2014-12-11

    cat << '_EOF_' > DEF
# human vs tarsier
# parameters obtained from a tuning run of lastz_D
# /hive/users/hiram/multiz/100way/hg38.tarSyr2/hg38.tarSyr2.tuning.top400.txt

BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.54/bin/lastz

BLASTZ_T=2
BLASTZ_O=400
BLASTZ_E=30
BLASTZ_M=50
BLASTZ_X=1000
BLASTZ_Y=3400
BLASTZ_Q=/hive/data/genomes/hg38/bed/lastzTarSyr2.2014-12-11/hg38.tarSyr2.tuning.Q.txt
#       A     C     G     T
# A   100  -172   -29  -118
# C  -172    98  -170   -29
# G   -29  -170    98  -172
# T  -118   -29  -172   100

# TARGET: Human hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LIMIT=80
SEQ1_LAP=10000

# QUERY: Tarsier tarSyr2
SEQ2_DIR=/hive/data/genomes/tarSyr2/tarSyr2.2bit
SEQ2_LEN=/hive/data/genomes/tarSyr2/chrom.sizes
SEQ2_CHUNK=20000000
SEQ2_LIMIT=500
SEQ2_LAP=0

BASE=/hive/data/genomes/hg38/bed/lastzTarSyr2.2014-12-11
TMPDIR=/dev/shm
'_EOF_'
    # << happy emacs

    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
        -chainMinScore=3000 -chainLinearGap=medium \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > do.log 2>&1
    # real    1223m11.846s

    cat fb.hg38.chainTarSyr2Link.txt
    # 1708294423 bases of 3049335806 (56.022%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` hg38 tarSyr2) > rbest.log 2>&1 &
    # real    46m29.975s
    time (doRecipBest.pl -load -continue=load -workhorse=hgwdev \
	-buildDir=`pwd` hg38 tarSyr2) > loadRBest.log 2>&1 &
    # real    12m28.565s

    cat fb.hg38.chainRBestTarSyr2Link.txt
    # 1563421915 bases of 3049335806 (51.271%) in intersection

    # create and load up syntenic chainNet: 2017-10-27
cd /hive/data/genomes/hg38/bed/lastzTarSyr2.2014-12-11/axtChain
netToAxt hg38.tarSyr2.syn.net.gz hg38.tarSyr2.all.chain.gz \
/scratch/data/hg38/hg38.2bit /hive/data/genomes/tarSyr2/tarSyr2.2bit stdout \
  | axtSort stdin stdout \
     | axtToChain stdin /hive/data/genomes/hg38/chrom.sizes \
        /hive/data/genomes/tarSyr2/chrom.sizes stdout \
            | gzip -c > hg38.tarSyr2.syn.chain.gz
hgLoadChain -tIndex hg38 chainSynTarSyr2 hg38.tarSyr2.syn.chain.gz
netFilter -minGap=10 hg38.tarSyr2.syn.net.gz \
  | hgLoadNet -verbose=0 hg38 netSynTarSyr2 stdin
cd /hive/data/genomes/hg38/bed/lastzTarSyr2.2014-12-11
featureBits hg38 chainSynTarSyr2Link > fb.hg38.chainSynTarSyr2Link.txt 2>&1
cat fb.hg38.chainSynTarSyr2Link.txt
# 1622913627 bases of 3049335806 (53.222%) in intersection

    # and for the swap:
    mkdir /hive/data/genomes/tarSyr2/bed/blastz.hg38.swap
    cd /hive/data/genomes/tarSyr2/bed/blastz.hg38.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/hg38/bed/lastzTarSyr2.2014-12-11/DEF \
        -swap -chainMinScore=3000 -chainLinearGap=medium \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    #  real    452m27.264s

    cat fb.tarSyr2.chainHg38Link.txt
    # 1781378574 bases of 3405755564 (52.305%) in intersection

    time (doRecipBest.pl -buildDir=`pwd` tarSyr2 hg38) > rbest.log 2>&1
    # real    115m47.619s

##############################################################################
# LASTZ Kangaroo Rat DipOrd2 (DONE - 2018-01-01 - Hiram)
    mkdir /hive/data/genomes/hg38/bed/lastzDipOrd2.2018-01-01
    cd /hive/data/genomes/hg38/bed/lastzDipOrd2.2018-01-01

    printf '# Human vs. Kangaroo Rat
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz
BLASTZ_O=400
BLASTZ_E=30
BLASTZ_M=254
# default BLASTZ_Q score matrix:
#       A     C     G     T
# A    91  -114   -31  -123
# C  -114   100  -125   -31
# G   -31  -125   100  -114
# T  -123   -31  -114    91

# TARGET: Human Hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CTGDIR=/hive/data/genomes/hg38/hg38.contigs.2bit
SEQ1_CTGLEN=/hive/data/genomes/hg38/hg38.contigs.chrom.sizes
SEQ1_LIFT=/hive/data/genomes/hg38/jkStuff/hg38.contigs.lift
SEQ1_CHUNK=20000000
SEQ1_LAP=10000

# QUERY: Kangaroo Rat
SEQ2_DIR=/hive/data/genomes/dipOrd2/dipOrd2.2bit
SEQ2_LEN=/hive/data/genomes/dipOrd2/chrom.sizes
SEQ2_CHUNK=20000000
SEQ2_LIMIT=180
SEQ2_LAP=0

BASE=/hive/data/genomes/hg38/bed/lastzDipOrd2.2018-01-01
TMPDIR=/dev/shm
' > DEF

    #	establish a screen to control this job
    screen
    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
        -chainMinScore=3000 -chainLinearGap=medium \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > do.log 2>&1 &
    #	real    435m37.638s

    cat fb.hg38.chainDipOrd2Link.txt
    # 1001007354 bases of 3049335806 (32.827%) in intersection
    cat fb.hg38.chainSynDipOrd2Link.txt
    # 934602735 bases of 3049335806 (30.649%) in intersection

    time (doRecipBest.pl -load -workhorse=hgwdev \
	-buildDir=`pwd` hg38 dipOrd2) > rbest.log 2>&1 &
    #	real    424m7.155s

    cat fb.hg38.chainRBestDipOrd2Link.txt
    # 921538020 bases of 3049335806 (30.221%) in intersection

    # and for the swap:
    mkdir /hive/data/genomes/dipOrd2/bed/blastz.hg38.swap
    cd /hive/data/genomes/dipOrd2/bed/blastz.hg38.swap
    time (doBlastzChainNet.pl -verbose=2 \
        /hive/data/genomes/hg38/bed/lastzDipOrd2.2018-01-01/DEF \
        -chainMinScore=3000 -chainLinearGap=medium \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -swap -syntenicNet) > swap.log 2>&1 &
    # real    97m8.750s

    cat fb.dipOrd2.chainHg38Link.txt
    # 957281496 bases of 2065314047 (46.350%) in intersection
    cat fb.dipOrd2.chainSynHg38Link.txt
    # 905805640 bases of 2065314047 (43.858%) in intersection

    time (doRecipBest.pl -load -workhorse=hgwdev \
	-buildDir=`pwd` dipOrd2 hg38) > rbest.log 2>&1 &
    # real    431m28.226s

    cat fb.dipOrd2.chainRBestHg38Link.txt
    # 923041001 bases of 2065314047 (44.693%) in intersection

##############################################################################
# LASTZ Damara mole rat - Fukomys damarensis (DONE - 2018-01-01 - Hiram)
    mkdir /hive/data/genomes/hg38/bed/lastzFukDam1.2018-01-01
    cd /hive/data/genomes/hg38/bed/lastzFukDam1.2018-01-01

    printf '# Human vs. Damara mole rat
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz
BLASTZ_O=400
BLASTZ_E=30
BLASTZ_M=254
# default BLASTZ_Q score matrix:
#       A     C     G     T
# A    91  -114   -31  -123
# C  -114   100  -125   -31
# G   -31  -125   100  -114
# T  -123   -31  -114    91

# TARGET: Human Hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CTGDIR=/hive/data/genomes/hg38/hg38.contigs.2bit
SEQ1_CTGLEN=/hive/data/genomes/hg38/hg38.contigs.chrom.sizes
SEQ1_LIFT=/hive/data/genomes/hg38/jkStuff/hg38.contigs.lift
SEQ1_CHUNK=20000000
SEQ1_LAP=10000

# QUERY: Damara mole rat
SEQ2_DIR=/hive/data/genomes/fukDam1/fukDam1.2bit
SEQ2_LEN=/hive/data/genomes/fukDam1/chrom.sizes
SEQ2_CHUNK=20000000
SEQ2_LIMIT=200
SEQ2_LAP=0

BASE=/hive/data/genomes/hg38/bed/lastzFukDam1.2018-01-01
TMPDIR=/dev/shm
' > DEF

    #	establish a screen to control this job
    screen
    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
        -chainMinScore=3000 -chainLinearGap=medium \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > do.log 2>&1 &
    #	real    504m13.875s

    cat fb.hg38.chainFukDam1Link.txt
    # 1340852960 bases of 3049335806 (43.972%) in intersection
    cat fb.hg38.chainSynFukDam1Link.txt
    # 1276966958 bases of 3049335806 (41.877%) in intersection

    time (doRecipBest.pl -load -workhorse=hgwdev \
	-buildDir=`pwd` hg38 fukDam1) > rbest.log 2>&1 &
    #	real    391m20.373s
    cat fb.hg38.chainRBestFukDam1Link.txt
    # 1236966410 bases of 3049335806 (40.565%) in intersection

    # and for the swap:
    mkdir /hive/data/genomes/fukDam1/bed/blastz.hg38.swap
    cd /hive/data/genomes/fukDam1/bed/blastz.hg38.swap
    time (doBlastzChainNet.pl -verbose=2 \
        /hive/data/genomes/hg38/bed/lastzFukDam1.2018-01-01/DEF \
        -chainMinScore=3000 -chainLinearGap=medium \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -swap -syntenicNet) > swap.log 2>&1 &
    # real    122m19.689s

    cat fb.fukDam1.chainHg38Link.txt
    # 1290829351 bases of 2285984782 (56.467%) in intersection
    cat fb.fukDam1.chainSynHg38Link.txt
    # 1233187886 bases of 2285984782 (53.946%) in intersection

    time (doRecipBest.pl -load -workhorse=hgwdev \
	-buildDir=`pwd` fukDam1 hg38) > rbest.log 2>&1 &
    # real    456m33.399s

    cat fb.fukDam1.chainRBestHg38Link.txt
    # 1238697651 bases of 2285984782 (54.187%) in intersection

##############################################################################
# Chimp Lastz run (DONE - 2018-01-03 - Hiram)
    screen -S hg38PanTro3      # use a screen to manage this longish running job
    mkdir /hive/data/genomes/hg38/bed/lastzPanTro3.2018-01-03
    cd /hive/data/genomes/hg38/bed/lastzPanTro3.2018-01-03

    # always set the BLASTZ program so we know what version was used
    printf "# human vs chimp
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz
BLASTZ_T=2
BLASTZ_O=600
BLASTZ_E=150
BLASTZ_M=254
BLASTZ_K=4500
BLASTZ_L=4500
BLASTZ_Y=15000
BLASTZ_Q=/scratch/data/blastz/human_chimp.v2.q
#    A    C    G    T
#    90 -330 -236 -356
#  -330  100 -318 -236
#  -236 -318  100 -330
#  -356 -236 -330   90

# TARGET: Human Hg38
SEQ1_DIR=/scratch/data/hg38/hg38.2bit
SEQ1_LEN=/scratch/data/hg38/chrom.sizes
SEQ1_CHUNK=40000000
SEQ1_LAP=10000
SEQ1_IN_CONTIGS=0

# QUERY: Chimp PanTro3
SEQ2_DIR=/hive/data/genomes/panTro3/panTro3.2bit
SEQ2_LEN=/hive/data/genomes/panTro3/chrom.sizes
SEQ2_CHUNK=20000000
SEQ2_LAP=0
SEQ2_LIMIT=100
SEQ2_IN_CONTIGS=0

BASE=/hive/data/genomes/hg38/bed/lastzPanTro3.2018-01-03
TMPDIR=/dev/shm
" > DEF

    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
        -chainMinScore=5000 -chainLinearGap=medium \
        -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
        -syntenicNet) > do.log 2>&1
    # real    170m54.660s

    cat fb.hg38.chainPanTro3Link.txt
    # 2839373050 bases of 3049335806 (93.114%) in intersection
    cat fb.hg38.chainSynPanTro3Link.txt
    # 2805471052 bases of 3049335806 (92.003%) in intersection

    # filter with doRecipBest.pl
    time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \
        hg38 panTro3) > rbest.log 2>&1
    # real    122m48.608s

    cat fb.hg38.chainRBestPanTro3Link.txt
    # 2677897807 bases of 3049335806 (87.819%) in intersection

    # running the swap
    mkdir /hive/data/genomes/panTro3/bed/blastz.hg38.swap
    cd /hive/data/genomes/panTro3/bed/blastz.hg38.swap
    time (doBlastzChainNet.pl -verbose=2 \
        -swap /hive/data/genomes/hg38/bed/lastzPanTro3.2018-01-03/DEF \
        -chainMinScore=5000 -chainLinearGap=medium \
        -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
        -syntenicNet) > swap.log 2>&1
    # real    92m7.154s

    cat fb.panTro3.chainHg38Link.txt
    # 2775323749 bases of 2900529764 (95.683%) in intersection

    cat fb.panTro3.chainSynHg38Link.txt
    # 2733818111 bases of 2900529764 (94.252%) in intersection

    time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \
        panTro3 hg38) > rbest.log 2>&1
    # real    173m38.562s

    cat fb.panTro3.chainRBestHg38Link.txt
    # 2685706565 bases of 2900529764 (92.594%) in intersection

#############################################################################
# LASTZ human/hg38 vs. Chinese hamster CHO-K1 cell line/criGriChoV2
#	(DONE - 2018-01-05 - Hiram)

    mkdir /hive/data/genomes/hg38/bed/lastzCriGriChoV2.2018-01-05
    cd /hive/data/genomes/hg38/bed/lastzCriGriChoV2.2018-01-05

    printf '# human vs Chinese hamster ovary CHO-K1 cell line
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz
BLASTZ_M=254

# TARGET: human hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CTGDIR=/hive/data/genomes/hg38/hg38.contigs.2bit
SEQ1_CTGLEN=/hive/data/genomes/hg38/hg38.contigs.chrom.sizes
SEQ1_LIFT=/hive/data/genomes/hg38/jkStuff/hg38.contigs.lift
SEQ1_CHUNK=40000000
SEQ1_LIMIT=20
SEQ1_LAP=10000

# QUERY: Chinese hamster ovary CHO-K1 cell line criGriChoV2
SEQ2_DIR=/hive/data/genomes/criGriChoV2/criGriChoV2.2bit
SEQ2_LEN=/hive/data/genomes/criGriChoV2/chrom.sizes
SEQ2_CHUNK=20000000
SEQ2_LIMIT=20
SEQ2_LAP=0

BASE=/hive/data/genomes/hg38/bed/lastzCriGriChoV2.2018-01-05
TMPDIR=/dev/shm
' > DEF

    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
        -chainMinScore=3000 -chainLinearGap=medium \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -noDbNameCheck -syntenicNet) > do.log 2>&1
    # real    527m7.679s

    cat fb.hg38.chainCriGriChoV2Link.txt
    # 1016328250 bases of 3049335806 (33.329%) in intersection
    cat fb.hg38.chainSynCriGriChoV2Link.txt
    # 961641546 bases of 3049335806 (31.536%) in intersection

    time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \
	hg38 criGriChoV2) > rbest.log 2>&1 &
    # real    443m50.337s

    cat fb.hg38.chainRBestCriGriChoV2Link.txt
    # 936450028 bases of 3049335806 (30.710%) in intersection

    # and for the swap:
    mkdir /hive/data/genomes/criGriChoV2/bed/blastz.hg38.swap
    cd /hive/data/genomes/criGriChoV2/bed/blastz.hg38.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/hg38/bed/lastzCriGriChoV2.2018-01-05/DEF \
        -swap -chainMinScore=3000 -chainLinearGap=medium \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -noDbNameCheck -syntenicNet) > swap.log 2>&1
    #  real    123m38.716s

    cat fb.criGriChoV2.chainHg38Link.txt
    # 983638905 bases of 2323924942 (42.327%) in intersection
    cat fb.criGriChoV2.chainSynHg38Link.txt
    # 932774807 bases of 2323924942 (40.138%) in intersection

    time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \
	criGriChoV2 hg38) > rbest.log 2>&1 &
    # real    489m43.438s

    cat fb.criGriChoV2.chainRBestHg38Link.txt
    # 938325634 bases of 2323924942 (40.377%) in intersection

#########################################################################
# LASTZ human/hg38 Baboon/papAnu4 - (DONE - 2018-01-08 - Hiram)
    mkdir /hive/data/genomes/hg38/bed/lastzPapAnu4.2018-01-08
    cd /hive/data/genomes/hg38/bed/lastzPapAnu4.2018-01-08

    printf '# human vs baboon
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz
BLASTZ_M=254

# TARGET: human hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CTGDIR=/hive/data/genomes/hg38/hg38.contigs.2bit
SEQ1_CTGLEN=/hive/data/genomes/hg38/hg38.contigs.chrom.sizes
SEQ1_LIFT=/hive/data/genomes/hg38/jkStuff/hg38.contigs.lift
SEQ1_CHUNK=40000000
SEQ1_LIMIT=10
SEQ1_LAP=10000

# QUERY: Baboon papAnu4
SEQ2_DIR=/hive/data/genomes/papAnu4/papAnu4.2bit
SEQ2_LEN=/hive/data/genomes/papAnu4/chrom.sizes
SEQ2_CHUNK=20000000
SEQ2_LIMIT=150
SEQ2_LAP=0

BASE=/hive/data/genomes/hg38/bed/lastzPapAnu4.2018-01-08
TMPDIR=/dev/shm
' > DEF

    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
        -chainMinScore=3000 -chainLinearGap=medium \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > do.log 2>&1 &
    # real    1300m59.182s

    cat fb.hg38.chainPapAnu4Link.txt
    # 2665048631 bases of 3049335806 (87.398%) in intersection

    time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` hg38 papAnu4) \
        > rbest.log 2>&1 &
    # real    394m33.277s

    cat fb.hg38.chainRBestPapAnu4Link.txt
    # 2462004619 bases of 3049335806 (80.739%) in intersection

    # and for the swap:
    mkdir /hive/data/genomes/papAnu4/bed/blastz.hg38.swap
    cd /hive/data/genomes/papAnu4/bed/blastz.hg38.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/hg38/bed/lastzPapAnu4.2018-01-08/DEF \
        -swap -chainMinScore=3000 -chainLinearGap=medium \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
          -syntenicNet) > swap.log 2>&1
    #  real    166m16.865s

    cat fb.papAnu4.chainHg38Link.txt
    # 2539481835 bases of 2937004939 (86.465%) in intersection
    cat fb.papAnu4.chainSynHg38Link.txt
    # 2485777123 bases of 2937004939 (84.636%) in intersection

    time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` papAnu4 hg38) \
      > rbest.log 2>&1 &
    # real    483m48.216s

    cat fb.papAnu4.chainRBestHg38Link.txt
    # 2465241931 bases of 2937004939 (83.937%) in intersection

#########################################################################
# LASTZ human/hg38 vs. guinea pig/cavApe1 - (DONE - 2018-01-08 - Hiram)
    mkdir /hive/data/genomes/hg38/bed/lastzCavApe1.2018-01-08
    cd /hive/data/genomes/hg38/bed/lastzCavApe1.2018-01-08

    printf '# human vs guinea pig
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz
BLASTZ_O=400
BLASTZ_E=30
BLASTZ_M=254
# default BLASTZ_Q score matrix:
#       A     C     G     T
# A    91  -114   -31  -123
# C  -114   100  -125   -31
# G   -31  -125   100  -114
# T  -123   -31  -114    91

# TARGET: human hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CTGDIR=/hive/data/genomes/hg38/hg38.contigs.2bit
SEQ1_CTGLEN=/hive/data/genomes/hg38/hg38.contigs.chrom.sizes
SEQ1_LIFT=/hive/data/genomes/hg38/jkStuff/hg38.contigs.lift
SEQ1_CHUNK=40000000
SEQ1_LIMIT=30
SEQ1_LAP=10000

# QUERY: guinea pig cavApe1
SEQ2_DIR=/hive/data/genomes/cavApe1/cavApe1.2bit
SEQ2_LEN=/hive/data/genomes/cavApe1/chrom.sizes
SEQ2_CHUNK=20000000
SEQ2_LIMIT=20
SEQ2_LAP=0

BASE=/hive/data/genomes/hg38/bed/lastzCavApe1.2018-01-08
TMPDIR=/dev/shm
' > DEF

    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
        -chainMinScore=3000 -chainLinearGap=medium \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > do.log 2>&1 &
    # real    502m28.460s

    cat fb.hg38.chainCavApe1Link.txt
    # 804449430 bases of 3049335806 (26.381%) in intersection
    cat fb.hg38.chainSynCavApe1Link.txt
    # 746370799 bases of 3049335806 (24.477%) in intersection

    time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \
	hg38 cavApe1) > rbest.log 2>&1 &
    # real    386m40.434s

    cat fb.hg38.chainRBestCavApe1Link.txt
    # 735739254 bases of 3049335806 (24.128%) in intersection

    # and for the swap:
    mkdir /hive/data/genomes/cavApe1/bed/blastz.hg38.swap
    cd /hive/data/genomes/cavApe1/bed/blastz.hg38.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/hg38/bed/lastzCavApe1.2018-01-08/DEF \
        -swap -chainMinScore=3000 -chainLinearGap=medium \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    #  real    61m35.236s

    cat fb.cavApe1.chainHg38Link.txt
    # 767670846 bases of 1749140834 (43.888%) in intersection
    cat fb.cavApe1.chainSynHg38Link.txt
    # 734822213 bases of 1749140834 (42.010%) in intersection

    time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \
	cavApe1 hg38) > rbest.log 2>&1
    # real    327m9.529s

    cat fb.cavApe1.chainRBestHg38Link.txt
    # 737288411 bases of 1749140834 (42.151%) in intersection

#########################################################################
# LASTZ human/hg38 vs. Collard flycatcher/ficAlb1 - (DONE - 2018-01-08 - Hiram)
    mkdir /hive/data/genomes/hg38/bed/lastzFicAlb1.2018-01-08
    cd /hive/data/genomes/hg38/bed/lastzFicAlb1.2018-01-08

    cat << '_EOF_' > DEF
    printf '# human vs Collard flycatcher
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz
BLASTZ_O=400
BLASTZ_E=30
BLASTZ_Y=3400
BLASTZ_L=6000
BLASTZ_K=2200
BLASTZ_M=50
BLASTZ_Q=/scratch/data/blastz/HoxD55.q
#      A    C    G    T
#     91  -90  -25 -100
#    -90  100 -100  -25
#    -25 -100  100  -90
#   -100  -25  -90  91

# TARGET: human hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CTGDIR=/hive/data/genomes/hg38/hg38.contigs.2bit
SEQ1_CTGLEN=/hive/data/genomes/hg38/hg38.contigs.chrom.sizes
SEQ1_LIFT=/hive/data/genomes/hg38/jkStuff/hg38.contigs.lift
SEQ1_CHUNK=40000000
SEQ1_LIMIT=30
SEQ1_LAP=10000

# QUERY: Collard flycatcher ficAlb1
SEQ2_DIR=/hive/data/genomes/ficAlb1/ficAlb1.2bit
SEQ2_LEN=/hive/data/genomes/ficAlb1/chrom.sizes
SEQ2_CHUNK=20000000
SEQ2_LIMIT=30
SEQ2_LAP=0

BASE=/hive/data/genomes/hg38/bed/lastzFicAlb1.2018-01-08
TMPDIR=/dev/shm
' > DEF

    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
        -chainMinScore=5000 -chainLinearGap=loose \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > do.log 2>&1 &
    # real    605m22.594s

    cat fb.hg38.chainFicAlb1Link.txt
    # 147048785 bases of 3049335806 (4.822%) in intersection
    cat fb.hg38.chainSynFicAlb1Link.txt
    # 88694039 bases of 3049335806 (2.909%) in intersection

    time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \
	hg38 ficAlb1) > rbest.log 2>&1 &
    # real    324m34.953s

    cat fb.hg38.chainRBestFicAlb1Link.txt
    # 103439671 bases of 3049335806 (3.392%) in intersection

    # and for the swap:
    mkdir /hive/data/genomes/ficAlb1/bed/blastz.hg38.swap
    cd /hive/data/genomes/ficAlb1/bed/blastz.hg38.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/hg38/bed/lastzFicAlb1.2018-01-08/DEF \
        -swap -chainMinScore=5000 -chainLinearGap=loose \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    #  real    14m32.727s

    cat fb.ficAlb1.chainHg38Link.txt
    # 118476285 bases of 1102325870 (10.748%) in intersection
    cat fb.ficAlb1.chainSynHg38Link.txt
    # 86852014 bases of 1102325870 (7.879%) in intersection

    time (doRecipBest.pl -load  -workhorse=hgwdev -buildDir=`pwd` \
	ficAlb1 hg38) > rbest.log 2>&1
    # real    265m12.990s

    cat fb.ficAlb1.chainRBestHg38Link.txt
    # 103174487 bases of 1102325870 (9.360%) in intersection

#########################################################################
# LASTZ human/hg38 vs. lamprey/petMar3 - (DONE - 2018-01-25 - Hiram)
    mkdir /hive/data/genomes/hg38/bed/lastzPetMar3.2018-01-25
    cd /hive/data/genomes/hg38/bed/lastzPetMar3.2018-01-25

    printf '# human vs lamprey
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz
BLASTZ_Y=3400
BLASTZ_L=6000
BLASTZ_K=2200
BLASTZ_M=50
BLASTZ_Q=/scratch/data/blastz/HoxD55.q
#      A    C    G    T
#     91  -90  -25 -100
#    -90  100 -100  -25
#    -25 -100  100  -90
#   -100  -25  -90  91

# TARGET: human hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CTGDIR=/hive/data/genomes/hg38/hg38.contigs.2bit
SEQ1_CTGLEN=/hive/data/genomes/hg38/hg38.contigs.chrom.sizes
SEQ1_LIFT=/hive/data/genomes/hg38/jkStuff/hg38.contigs.lift
SEQ1_CHUNK=40000000
SEQ1_LIMIT=3
SEQ1_LAP=10000

# QUERY: lamprey petMar3
SEQ2_DIR=/hive/data/genomes/petMar3/petMar3.2bit
SEQ2_LEN=/hive/data/genomes/petMar3/chrom.sizes
SEQ2_CHUNK=20000000
SEQ2_LIMIT=100
SEQ2_LAP=0

BASE=/hive/data/genomes/hg38/bed/lastzPetMar3.2018-01-25
TMPDIR=/dev/shm
' > DEF

    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
        -chainMinScore=5000 -chainLinearGap=loose \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > do.log 2>&1
    # real    117m35.788s

    cat fb.hg38.chainPetMar3Link.txt
    # 52661859 bases of 3049335806 (1.727%) in intersection

    cat fb.hg38.chainSynPetMar3Link.txt
    # 1508338 bases of 3049335806 (0.049%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -load -buildDir=`pwd` hg38 petMar3) \
	> rbest.log 2>&1 &
    # real    259m50.083s

    cat fb.hg38.chainRBestPetMar3Link.txt
    # 25411380 bases of 3049335806 (0.833%) in intersection

    # and for the swap:
    mkdir /hive/data/genomes/petMar3/bed/blastz.hg38.swap
    cd /hive/data/genomes/petMar3/bed/blastz.hg38.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/hg38/bed/lastzPetMar3.2018-01-25/DEF \
        -swap -chainMinScore=5000 -chainLinearGap=loose \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    #  real    12m51.092s

    cat fb.petMar3.chainHg38Link.txt
    # 51300303 bases of 1043181598 (4.918%) in intersection

    cat fb.petMar3.chainSynHg38Link.txt
    # 1425757 bases of 1043181598 (0.137%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -load -buildDir=`pwd` petMar3 hg38) \
	> rbest.log 2>&1 &
    # real    264m26.880s

    cat fb.petMar3.chainRBestHg38Link.txt
    # 25154743 bases of 1043181598 (2.411%) in intersection

#########################################################################
# LASTZ human/hg38 vs. garter snake/thaSir1 - (DONE - 2018-02-13 - Hiram)
    mkdir /hive/data/genomes/hg38/bed/lastzThaSir1.2018-02-13
    cd /hive/data/genomes/hg38/bed/lastzThaSir1.2018-02-13

    # note: first time with this new 1.04.00 version of lastz

    printf '# human vs garter snake
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.00/bin/lastz
BLASTZ_Y=3400
BLASTZ_L=6000
BLASTZ_K=2200
BLASTZ_M=50
BLASTZ_Q=/scratch/data/blastz/HoxD55.q
#      A    C    G    T
#     91  -90  -25 -100
#    -90  100 -100  -25
#    -25 -100  100  -90
#   -100  -25  -90  91

# TARGET: human hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CTGDIR=/hive/data/genomes/hg38/hg38.contigs.2bit
SEQ1_CTGLEN=/hive/data/genomes/hg38/hg38.contigs.chrom.sizes
SEQ1_LIFT=/hive/data/genomes/hg38/jkStuff/hg38.contigs.lift
SEQ1_CHUNK=40000000
SEQ1_LIMIT=3
SEQ1_LAP=10000

# QUERY: garter snake thaSir1
SEQ2_DIR=/hive/data/genomes/thaSir1/thaSir1.2bit
SEQ2_LEN=/hive/data/genomes/thaSir1/chrom.sizes
SEQ2_CHUNK=20000000
SEQ2_LIMIT=28
SEQ2_LAP=0

BASE=/hive/data/genomes/hg38/bed/lastzThaSir1.2018-02-13
TMPDIR=/dev/shm
' > DEF

    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
        -chainMinScore=5000 -chainLinearGap=loose \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > do.log 2>&1
    # real    124m58.650s

    cat fb.hg38.chainThaSir1Link.txt
    # 99838535 bases of 3049335806 (3.274%) in intersection

    cat fb.hg38.chainSynThaSir1Link.txt
    # 29432396 bases of 3049335806 (0.965%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -load -buildDir=`pwd` hg38 thaSir1)\
	> rbest.log 2>&1 &
    # real    315m43.227s

    cat fb.hg38.chainRBestThaSir1Link.txt
    # 66452884 bases of 3049335806 (2.179%) in intersection

    # and for the swap:
    mkdir /hive/data/genomes/thaSir1/bed/blastz.hg38.swap
    cd /hive/data/genomes/thaSir1/bed/blastz.hg38.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/hg38/bed/lastzThaSir1.2018-02-13/DEF \
        -swap -chainMinScore=5000 -chainLinearGap=loose \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1 &
    #  real    16m52.956s

    cat fb.thaSir1.chainHg38Link.txt
    # 75915958 bases of 1122701795 (6.762%) in intersection

    cat fb.thaSir1.chainSynHg38Link.txt
    # 28865261 bases of 1122701795 (2.571%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -load -buildDir=`pwd` thaSir1 hg38)\
	 > rbest.log 2>&1
    # real    269m56.160s

    cat fb.thaSir1.chainRBestHg38Link.txt
    # 66545073 bases of 1122701795 (5.927%) in intersection

#########################################################################
# LASTZ human/hg38 vs. cat/felCat9 - (DONE - 2018-03-14 - Hiram)
    mkdir /hive/data/genomes/hg38/bed/lastzFelCat9.2018-03-14
    cd /hive/data/genomes/hg38/bed/lastzFelCat9.2018-03-14

    # note: first time with this new 1.04.00 version of lastz

    printf '# human vs cat
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.00/bin/lastz
BLASTZ_O=400
BLASTZ_E=30
BLASTZ_M=254
# default BLASTZ_Q score matrix:
#       A     C     G     T
# A    91  -114   -31  -123
# C  -114   100  -125   -31
# G   -31  -125   100  -114
# T  -123   -31  -114    91

# TARGET: human hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CTGDIR=/hive/data/genomes/hg38/hg38.contigs.2bit
SEQ1_CTGLEN=/hive/data/genomes/hg38/hg38.contigs.chrom.sizes
SEQ1_LIFT=/hive/data/genomes/hg38/jkStuff/hg38.contigs.lift
SEQ1_CHUNK=40000000
SEQ1_LIMIT=30
SEQ1_LAP=10000

# QUERY: cat felCat9
SEQ2_DIR=/hive/data/genomes/felCat9/felCat9.2bit
SEQ2_LEN=/hive/data/genomes/felCat9/chrom.sizes
SEQ2_CHUNK=20000000
SEQ2_LIMIT=100
SEQ2_LAP=0

BASE=/hive/data/genomes/hg38/bed/lastzFelCat9.2018-03-14
TMPDIR=/dev/shm
' > DEF

    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
        -chainMinScore=3000 -chainLinearGap=medium \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > do.log 2>&1
    # real    1256m48.240s

    cat fb.hg38.chainFelCat9Link.txt
    # 1579231929 bases of 3049335806 (51.789%) in intersection
    cat fb.hg38.chainSynFelCat9Link.txt
    # 1516804589 bases of 3049335806 (49.742%) in intersection

    time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` hg38 \
	felCat9) > rbest.log 2>&1 &
    # real    704m43.342s

    cat fb.hg38.chainRBestFelCat9Link.txt
    # 1449222744 bases of 3049335806 (47.526%) in intersection

    # and for the swap:
    mkdir /hive/data/genomes/felCat9/bed/blastz.hg38.swap
    cd /hive/data/genomes/felCat9/bed/blastz.hg38.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/hg38/bed/lastzFelCat9.2018-03-14/DEF \
        -swap -chainMinScore=3000 -chainLinearGap=medium \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    #  real    142m37.100s

    cat fb.felCat9.chainHg38Link.txt
    # 1486134443 bases of 2476453204 (60.011%) in intersection
    cat fb.felCat9.chainSynHg38Link.txt
    # 1452577988 bases of 2476453204 (58.656%) in intersection


    time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \
	felCat9 hg38) > rbest.log 2>&1 &
    # real    623m28.676s

    cat fb.felCat9.chainRBestHg38Link.txt
    # 1449521349 bases of 2476453204 (58.532%) in intersection

##############################################################################
# LASTZ Beaver casCan1 (DONE - 2018-03-19 - Hiram)
    mkdir /hive/data/genomes/hg38/bed/lastzCasCan1.2018-03-19
    cd /hive/data/genomes/hg38/bed/lastzCasCan1.2018-03-19

    # note: first time with this new 1.04.00 version of lastz

    printf '# Human vs. Beaver
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.00/bin/lastz
BLASTZ_O=400
BLASTZ_E=30
BLASTZ_M=254
# default BLASTZ_Q score matrix:
#       A     C     G     T
# A    91  -114   -31  -123
# C  -114   100  -125   -31
# G   -31  -125   100  -114
# T  -123   -31  -114    91

# TARGET: Human Hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CTGDIR=/hive/data/genomes/hg38/hg38.contigs.2bit
SEQ1_CTGLEN=/hive/data/genomes/hg38/hg38.contigs.chrom.sizes
SEQ1_LIFT=/hive/data/genomes/hg38/jkStuff/hg38.contigs.lift
SEQ1_CHUNK=20000000
SEQ1_LIMIT=80
SEQ1_LAP=10000

# QUERY: Beaver
SEQ2_DIR=/hive/data/genomes/casCan1/casCan1.2bit
SEQ2_LEN=/hive/data/genomes/casCan1/chrom.sizes
SEQ2_CHUNK=20000000
SEQ2_LIMIT=80
SEQ2_LAP=0

BASE=/hive/data/genomes/hg38/bed/lastzCasCan1.2018-03-19
TMPDIR=/dev/shm
' > DEF

    #	establish a screen to control this job
    screen
    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
        -chainMinScore=3000 -chainLinearGap=medium \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > do.log 2>&1 &
    #	real    568m56.951s

    cat fb.hg38.chainCasCan1Link.txt
    # 1440538496 bases of 3049335806 (47.241%) in intersection
    cat fb.hg38.chainSynCasCan1Link.txt
    # 1348638697 bases of 3049335806 (44.227%) in intersection

    time (doRecipBest.pl -load -workhorse=hgwdev \
	-buildDir=`pwd` hg38 casCan1) > rbest.log 2>&1 &
    #	real    903m29.785s

    cat fb.hg38.chainRBestCasCan1Link.txt
    # 1318039475 bases of 3049335806 (43.224%) in intersection

    # and for the swap:
    mkdir /hive/data/genomes/casCan1/bed/blastz.hg38.swap
    cd /hive/data/genomes/casCan1/bed/blastz.hg38.swap
    time (doBlastzChainNet.pl -verbose=2 \
        /hive/data/genomes/hg38/bed/lastzCasCan1.2018-03-19/DEF \
        -chainMinScore=3000 -chainLinearGap=medium \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -swap -syntenicNet) > swap.log 2>&1 &
    # real    141m44.555s

    cat fb.casCan1.chainHg38Link.txt
    # 1440839903 bases of 2517974654 (57.222%) in intersection
    cat fb.casCan1.chainSynHg38Link.txt
    # 1348477433 bases of 2517974654 (53.554%) in intersection

    time (doRecipBest.pl -load -workhorse=hgwdev \
	-buildDir=`pwd` casCan1 hg38) > rbest.log 2>&1 &
    # real    1199m30.336s

    cat fb.casCan1.chainRBestHg38Link.txt
    # 1321240715 bases of 2517974654 (52.472%) in intersection

##############################################################################
# Chimp Lastz run (DONE - 2018-03-24 - Hiram)
    screen -S hg38PanTro6      # use a screen to manage this longish running job
    mkdir /hive/data/genomes/hg38/bed/lastzPanTro6.2018-03-24
    cd /hive/data/genomes/hg38/bed/lastzPanTro6.2018-03-24

    # always set the BLASTZ program so we know what version was used
    printf "# human vs chimp
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.00/bin/lastz
BLASTZ_T=2
BLASTZ_O=600
BLASTZ_E=150
BLASTZ_M=254
BLASTZ_K=4500
BLASTZ_L=4500
BLASTZ_Y=15000
BLASTZ_Q=/scratch/data/blastz/human_chimp.v2.q
#    A    C    G    T
#    90 -330 -236 -356
#  -330  100 -318 -236
#  -236 -318  100 -330
#  -356 -236 -330   90

# TARGET: Human Hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CTGDIR=/hive/data/genomes/hg38/hg38.contigs.2bit
SEQ1_CTGLEN=/hive/data/genomes/hg38/hg38.contigs.chrom.sizes
SEQ1_LIFT=/hive/data/genomes/hg38/jkStuff/hg38.contigs.lift
SEQ1_CHUNK=20000000
SEQ1_LIMIT=50
SEQ1_LAP=10000

# QUERY: Chimp PanTro6
SEQ2_DIR=/hive/data/genomes/panTro6/panTro6.2bit
SEQ2_LEN=/hive/data/genomes/panTro6/chrom.sizes
SEQ2_CHUNK=20000000
SEQ2_LAP=0
SEQ2_LIMIT=50
SEQ2_IN_CONTIGS=0

BASE=/hive/data/genomes/hg38/bed/lastzPanTro6.2018-03-24
TMPDIR=/dev/shm
" > DEF

    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
        -chainMinScore=5000 -chainLinearGap=medium \
        -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
        -syntenicNet) > do.log 2>&1 &
    # real    239m0.367s

    cat fb.hg38.chainPanTro6Link.txt
    # 2910625246 bases of 3049335806 (95.451%) in intersection
    cat fb.hg38.chainSynPanTro6Link.txt
    # 2890994068 bases of 3049335806 (94.807%) in intersection

    # filter with doRecipBest.pl
    time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \
        hg38 panTro6) > rbest.log 2>&1
    # real    103m42.148s

    cat fb.hg38.chainRBestPanTro6Link.txt
    # 2743876160 bases of 3049335806 (89.983%) in intersection

    # running the swap
    mkdir /hive/data/genomes/panTro6/bed/blastz.hg38.swap
    cd /hive/data/genomes/panTro6/bed/blastz.hg38.swap
    time (doBlastzChainNet.pl -verbose=2 \
        -swap /hive/data/genomes/hg38/bed/lastzPanTro6.2018-03-24/DEF \
        -chainMinScore=5000 -chainLinearGap=medium \
        -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
        -syntenicNet) > swap.log 2>&1
    # real    101m29.782s

    cat fb.panTro6.chainHg38Link.txt
    # 2814507414 bases of 3018592990 (93.239%) in intersection
    cat fb.panTro6.chainSynHg38Link.txt
    # 2800642800 bases of 3018592990 (92.780%) in intersection

    time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \
        panTro6 hg38) > rbest.log 2>&1 &
    # real    102m47.533s

    cat fb.panTro6.chainRBestHg38Link.txt
    # 2748571185 bases of 3018592990 (91.055%) in intersection

##############################################################################
# Orangutan Lastz run (DONE - 2018-03-26 - Hiram)
    screen -S hg38PonAbe3      # use a screen to manage this longish running job
    mkdir /hive/data/genomes/hg38/bed/lastzPonAbe3.2018-03-26
    cd /hive/data/genomes/hg38/bed/lastzPonAbe3.2018-03-26

    # always set the BLASTZ program so we know what version was used
    printf "# human vs orangutan
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.00/bin/lastz
BLASTZ_T=2
BLASTZ_O=600
BLASTZ_E=150
BLASTZ_M=254
BLASTZ_K=4500
BLASTZ_L=4500
BLASTZ_Y=15000
BLASTZ_Q=/scratch/data/blastz/human_chimp.v2.q
#    A    C    G    T
#    90 -330 -236 -356
#  -330  100 -318 -236
#  -236 -318  100 -330
#  -356 -236 -330   90

# TARGET: Human Hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CTGDIR=/hive/data/genomes/hg38/hg38.contigs.2bit
SEQ1_CTGLEN=/hive/data/genomes/hg38/hg38.contigs.chrom.sizes
SEQ1_LIFT=/hive/data/genomes/hg38/jkStuff/hg38.contigs.lift
SEQ1_CHUNK=20000000
SEQ1_LIMIT=20
SEQ1_LAP=10000

# QUERY: Orangutan PonAbe3
SEQ2_DIR=/hive/data/genomes/ponAbe3/ponAbe3.2bit
SEQ2_LEN=/hive/data/genomes/ponAbe3/chrom.sizes
SEQ2_CHUNK=20000000
SEQ2_LAP=0
SEQ2_LIMIT=20
SEQ2_IN_CONTIGS=0

BASE=/hive/data/genomes/hg38/bed/lastzPonAbe3.2018-03-26
TMPDIR=/dev/shm
" > DEF

    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
        -chainMinScore=5000 -chainLinearGap=medium \
        -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
        -syntenicNet) > do.log 2>&1 &
    # real    282m16.272s

    cat fb.hg38.chainPonAbe3Link.txt
    # 2823472924 bases of 3049335806 (92.593%) in intersection
    cat fb.hg38.chainSynPonAbe3Link.txt
    # 2800840721 bases of 3049335806 (91.851%) in intersection

    # filter with doRecipBest.pl
    time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \
        hg38 ponAbe3) > rbest.log 2>&1 &
    # real    129m13.848s

    cat fb.hg38.chainRBestPonAbe3Link.txt
    # 2640015618 bases of 3049335806 (86.577%) in intersection

    # running the swap
    mkdir /hive/data/genomes/ponAbe3/bed/blastz.hg38.swap
    cd /hive/data/genomes/ponAbe3/bed/blastz.hg38.swap
    time (doBlastzChainNet.pl -verbose=2 \
        -swap /hive/data/genomes/hg38/bed/lastzPonAbe3.2018-03-26/DEF \
        -chainMinScore=5000 -chainLinearGap=medium \
        -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
        -syntenicNet) > swap.log 2>&1
    # real    92m31.689s

    cat fb.ponAbe3.chainHg38Link.txt
    # 2693373164 bases of 3043444524 (88.498%) in intersection
    cat fb.ponAbe3.chainSynHg38Link.txt
    # 2679121264 bases of 3043444524 (88.029%) in intersection

    time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \
        ponAbe3 hg38) > rbest.log 2>&1 &
    # real    141m23.715s

    cat fb.ponAbe3.chainRBestHg38Link.txt
    # 2641871600 bases of 3043444524 (86.805%) in intersection

#############################################################################
# LASTZ human/hg38 vs. sheep/oviAri4 - (DONE - 2018-04-25 - ChrisL)
    mkdir /hive/data/genomes/hg38/bed/lastzOviAri4.2018-04-25
    cd /hive/data/genomes/hg38/bed/lastzOviAri4.2018-04-25

    printf '# human vs sheep
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.00/bin/lastz
BLASTZ_T=2
BLASTZ_O=400
BLASTZ_E=30
BLASTZ_M=254
# default BLASTZ_Q score matrix:
#       A     C     G     T
# A    91  -114   -31  -123
# C  -114   100  -125   -31
# G   -31  -125   100  -114
# T  -123   -31  -114    91

# TARGET: human hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CTGDIR=/hive/data/genomes/hg38/hg38.contigs.2bit
SEQ1_CTGLEN=/hive/data/genomes/hg38/hg38.contigs.chrom.sizes
SEQ1_LIFT=/hive/data/genomes/hg38/jkStuff/hg38.contigs.lift
SEQ1_CHUNK=40000000
SEQ1_LIMIT=5
SEQ1_LAP=10000

# QUERY: Sheep oviAri4
SEQ2_DIR=/hive/data/genomes/oviAri4/oviAri4.2bit
SEQ2_LEN=/hive/data/genomes/oviAri4/chrom.sizes
SEQ2_CHUNK=20000000
SEQ2_LIMIT=40
SEQ2_LAP=0

BASE=/hive/data/genomes/hg38/bed/lastzOviAri4.2018-04-25
TMPDIR=/dev/shm
' > DEF
    # << happy emacs

    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
        -chainMinScore=3000 -chainLinearGap=medium \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > do.log 2>&1

    # lineCount: Undefined variable.
    # Command failed:
    # ssh -x -o 'StrictHostKeyChecking = no' -o 'BatchMode = yes' hgwdev \
    #   nice /hive/data/genomes/hg38/bed/lastzOviAri4.2018-04-25/axtChain/netSynteny.csh
    #
    # real  1423m22.844s

    # this took forever because the final job was stuck all night
    # and the syntenic net step failed, so remove the files and run
    # again, just like what happened for mm10:

    rm hg38.oviAri4.syn.chain.gz
    rm hg38.oviAri4.syn.net.gz

    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
        -continue=syntenicNet \
        -chainMinScore=3000 -chainLinearGap=medium \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > syntenicNet.log 2>&1 &
    # real    34m23.191s

    cat fb.hg38.chainOviAri4Link.txt
    # 1388649593 bases of 3049335806 (45.539%) in intersection

    time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` hg38 oviAri4) > rbest.log 2>&1 &
    # real    612m50.394s

    # and for the swap:
    mkdir /hive/data/genomes/oviAri4/bed/blastz.hg38.swap
    cd /hive/data/genomes/oviAri4/bed/blastz.hg38.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/hg38/bed/lastzOviAri4.2018-04-25/DEF \
        -swap -chainMinScore=3000 -chainLinearGap=medium \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1 &
    #  real    104m31.748s

    cat fb.oviAri4.chainHg38Link.txt
    # 1319553403 bases of 2587515673 (50.997%) in intersection
    # replacing the previous tuned version:
    # 1193048482 bases of 2534335866 (47.075%) in intersection

    time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` oviAri4 hg38) > rbest.log 2>&1 &
    # real    638m15.603s

#############################################################################
# LASTZ human/hg38 vs. horse/equCab3 - (DONE - 2018-05-25 - ChrisL)
    mkdir /hive/data/genomes/hg38/bed/lastzEquCab3.2018-05-25
    cd /hive/data/genomes/hg38/bed/lastzEquCab3.2018-05-25

    printf '# human vs horse
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.00/bin/lastz
BLASTZ_T=2
BLASTZ_O=400
BLASTZ_E=30
BLASTZ_M=254
# default BLASTZ_Q score matrix:
#       A     C     G     T
# A    91  -114   -31  -123
# C  -114   100  -125   -31
# G   -31  -125   100  -114
# T  -123   -31  -114    91

# TARGET: human hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CTGDIR=/hive/data/genomes/hg38/hg38.contigs.2bit
SEQ1_CTGLEN=/hive/data/genomes/hg38/hg38.contigs.chrom.sizes
SEQ1_LIFT=/hive/data/genomes/hg38/jkStuff/hg38.contigs.lift
SEQ1_CHUNK=40000000
SEQ1_LIMIT=5
SEQ1_LAP=10000

# QUERY: horse equCab3
SEQ2_DIR=/hive/data/genomes/equCab3/equCab3.2bit
SEQ2_LEN=/hive/data/genomes/equCab3/chrom.sizes
SEQ2_CHUNK=20000000
SEQ2_LIMIT=20
SEQ2_LAP=0

BASE=/hive/data/genomes/hg38/bed/lastzEquCab3.2018-05-25
TMPDIR=/dev/shm
' > DEF
    # << happy emacs

    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
        -chainMinScore=3000 -chainLinearGap=medium \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > do.log 2>&1
    # real    519m22.432s

    cat fb.hg38.chainEquCab3Link.txt
    # 1705190736 bases of 3049335806 (55.920%) in intersection

    cat fb.hg38.chainSynEquCab3Link.txt
    # 1642798373 bases of 3049335806 (53.874%) in intersection

    time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` hg38 equCab3) > rbest.log 2>&1 &
    # real    553m32.545s

    cat fb.hg38.chainRBest.EquCab3.txt
    # 1563820848 bases of 3049335806 (51.284%) in intersection

    # and for the swap:
    mkdir /hive/data/genomes/equCab3/bed/blastz.hg38.swap
    cd /hive/data/genomes/equCab3/bed/blastz.hg38.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/hg38/bed/lastzEquCab3.2018-05-25/DEF \
        -swap -chainMinScore=3000 -chainLinearGap=medium \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1 &
    #  real    122m26.771s

    cat fb.equCab3.chainHg38Link.txt
    # 1666879638 bases of 2497530654 (66.741%) in intersection

    cat fb.equCab3.chainSynHg38Link.txt
    # 1624977128 bases of 2497530654 (65.063%) in intersection

    time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` equCab3 hg38) > rbest.log 2>&1 &
    # real    473m11.347s

    cat fb.equCab3.chainRBest.Hg38.txt

#############################################################################
# LASTZ human/hg38 vs. Minke whale/balAcu1 - (DONE - 2018-06-11 - Hiram)
    mkdir /hive/data/genomes/hg38/bed/lastzBalAcu1.2018-06-11
    cd /hive/data/genomes/hg38/bed/lastzBalAcu1.2018-06-11

    printf '# human vs Minke whale
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.00/bin/lastz
BLASTZ_T=2
BLASTZ_O=400
BLASTZ_E=30
BLASTZ_M=254
# default BLASTZ_Q score matrix:
#       A     C     G     T
# A    91  -114   -31  -123
# C  -114   100  -125   -31
# G   -31  -125   100  -114
# T  -123   -31  -114    91

# TARGET: human hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CTGDIR=/hive/data/genomes/hg38/hg38.contigs.2bit
SEQ1_CTGLEN=/hive/data/genomes/hg38/hg38.contigs.chrom.sizes
SEQ1_LIFT=/hive/data/genomes/hg38/jkStuff/hg38.contigs.lift
SEQ1_CHUNK=40000000
SEQ1_LIMIT=5
SEQ1_LAP=10000

# QUERY: Minke whale balAcu1
SEQ2_DIR=/hive/data/genomes/balAcu1/balAcu1.2bit
SEQ2_LEN=/hive/data/genomes/balAcu1/chrom.sizes
SEQ2_CHUNK=20000000
SEQ2_LIMIT=40
SEQ2_LAP=0

BASE=/hive/data/genomes/hg38/bed/lastzBalAcu1.2018-06-11
TMPDIR=/dev/shm
' > DEF

    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
        -chainMinScore=3000 -chainLinearGap=medium \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > do.log 2>&1
    # real    226m14.103s

    cat fb.hg38.chainBalAcu1Link.txt
    # 1571134497 bases of 3049335806 (51.524%) in intersection

    cat fb.hg38.chainSynBalAcu1Link.txt
    # 1509091721 bases of 3049335806 (49.489%) in intersection

    time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` hg38 balAcu1) > rbest.log 2>&1 &
    # real    426m33.828s

    cat fb.hg38.chainRBest.BalAcu1.txt
    # 1443423443 bases of 3049335806 (47.336%) in intersection

    # and for the swap:
    mkdir /hive/data/genomes/balAcu1/bed/blastz.hg38.swap
    cd /hive/data/genomes/balAcu1/bed/blastz.hg38.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/hg38/bed/lastzBalAcu1.2018-06-11/DEF \
        -swap -chainMinScore=3000 -chainLinearGap=medium \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1 &
    #  real    105m38.443s

    cat fb.balAcu1.chainHg38Link.txt
    # 1485701363 bases of 2286657046 (64.973%) in intersection

    cat fb.balAcu1.chainSynHg38Link.txt
    # 1444079345 bases of 2286657046 (63.152%) in intersection

    time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` balAcu1 hg38) > rbest.log 2>&1 &
    # real    422m43.817s

    cat fb.balAcu1.chainRBest.Hg38.txt
    # 1443200492 bases of 2286657046 (63.114%) in intersection

#############################################################################
# LASTZ human/hg38 vs. Axolotl/ambMex1 - (DONE - 2018-07-09 - Hiram)
    mkdir /hive/data/genomes/hg38/bed/lastzAmbMex1.2018-07-09
    cd /hive/data/genomes/hg38/bed/lastzAmbMex1.2018-07-09

    printf '# human vs Axolotl
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.00/bin/lastz
BLASTZ_T=2
BLASTZ_O=400
BLASTZ_E=30
BLASTZ_M=254
# default BLASTZ_Q score matrix:
#       A     C     G     T
# A    91  -114   -31  -123
# C  -114   100  -125   -31
# G   -31  -125   100  -114
# T  -123   -31  -114    91

# TARGET: human hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CTGDIR=/hive/data/genomes/hg38/hg38.contigs.2bit
SEQ1_CTGLEN=/hive/data/genomes/hg38/hg38.contigs.chrom.sizes
SEQ1_LIFT=/hive/data/genomes/hg38/jkStuff/hg38.contigs.lift
SEQ1_CHUNK=40000000
SEQ1_LIMIT=5
SEQ1_LAP=10000

# QUERY: Axolotl ambMex1
SEQ2_DIR=/hive/data/genomes/ambMex1/ambMex1.2bit
SEQ2_LEN=/hive/data/genomes/ambMex1/chrom.sizes
SEQ2_CHUNK=80000000
SEQ2_LIMIT=800
SEQ2_LAP=0

BASE=/hive/data/genomes/hg38/bed/lastzAmbMex1.2018-07-09
TMPDIR=/dev/shm
' > DEF

    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
        -chainMinScore=5000 -chainLinearGap=loose \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > do.log 2>&1
    # real    226m14.103s

    cat fb.hg38.chainAmbMex1Link.txt
    # 54520910 bases of 3049335806 (1.788%) in intersection

    cat fb.hg38.chainSynAmbMex1Link.txt
    # 3343407 bases of 3049335806 (0.110%) in intersection

    time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` hg38 ambMex1) > rbest.log 2>&1 &
    # real    497m40.060s

    cat fb.hg38.chainRBest.AmbMex1.txt
    # 37383183 bases of 3049335806 (1.226%) in intersection

    # and for the swap:
    mkdir /hive/data/genomes/ambMex1/bed/blastz.hg38.swap
    cd /hive/data/genomes/ambMex1/bed/blastz.hg38.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/hg38/bed/lastzAmbMex1.2018-07-09/DEF \
        -swap -chainMinScore=5000 -chainLinearGap=loose \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1 &
    #  real    39m37.460s

    cat fb.ambMex1.chainHg38Link.txt
    # 59846443 bases of 28366694468 (0.211%) in intersection

    cat fb.ambMex1.chainSynHg38Link.txt
    # 3456707 bases of 28366694468 (0.012%) in intersection

    time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` ambMex1 hg38) > rbest.log 2>&1 &
    #  real    555m51.873s

    cat fb.ambMex1.chainRBest.Hg38.txt
    # 38573370 bases of 28366694468 (0.136%) in intersection

#############################################################################
# LASTZ human/hg38 vs. chicken/galGal6 - (DONE - 2018-10-12 - Hiram)
    mkdir /hive/data/genomes/hg38/bed/lastzGalGal6.2018-10-12
    cd /hive/data/genomes/hg38/bed/lastzGalGal6.2018-10-12

    printf "# human vs chicken
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.00/bin/lastz
BLASTZ_O=400
BLASTZ_E=30
BLASTZ_Y=3400
BLASTZ_L=6000
BLASTZ_K=2200
BLASTZ_M=50
BLASTZ_Q=/scratch/data/blastz/HoxD55.q
#      A    C    G    T
#     91  -90  -25 -100
#    -90  100 -100  -25
#    -25 -100  100  -90
#   -100  -25  -90  91

# TARGET: human hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CTGDIR=/hive/data/genomes/hg38/hg38.contigs.2bit
SEQ1_CTGLEN=/hive/data/genomes/hg38/hg38.contigs.chrom.sizes
SEQ1_LIFT=/hive/data/genomes/hg38/jkStuff/hg38.contigs.lift
SEQ1_CHUNK=40000000
SEQ1_LIMIT=30
SEQ1_LAP=10000

# QUERY: chicken galGal6
SEQ2_DIR=/hive/data/genomes/galGal6/galGal6.2bit
SEQ2_LEN=/hive/data/genomes/galGal6/chrom.sizes
SEQ2_CHUNK=20000000
SEQ2_LIMIT=30
SEQ2_LAP=0

BASE=/hive/data/genomes/hg38/bed/lastzGalGal6.2018-10-12
TMPDIR=/dev/shm
" > DEF
    # << happy emacs

    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
        -chainMinScore=5000 -chainLinearGap=loose \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > do.log 2>&1
    # real    83m10.878s

    cat fb.hg38.chainGalGal6Link.txt
    # 154079940 bases of 3095998939 (4.977%) in intersection

    cat fb.hg38.chainSynGalGal6Link.txt
    # 95877644 bases of 3095998939 (3.097%) in intersection

    time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` hg38 galGal6) > rbest.log 2>&1 &
    # real    154m32.367s

    cat fb.hg38.chainRBest.GalGal6.txt
    # 106665747 bases of 3095998939 (3.445%) in intersection

    # and for the swap:
    mkdir /hive/data/genomes/galGal6/bed/blastz.hg38.swap
    cd /hive/data/genomes/galGal6/bed/blastz.hg38.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/hg38/bed/lastzGalGal6.2018-10-12/DEF \
        -swap -chainMinScore=5000 -chainLinearGap=loose \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    #  real    9m45.514s

    cat fb.galGal6.chainHg38Link.txt
    # 120955955 bases of 1055588482 (11.459%) in intersection

    cat fb.galGal6.chainSynHg38Link.txt
    # 92597630 bases of 1055588482 (8.772%) in intersection

    time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` galGal6 hg38) > rbest.log 2>&1 &
    # real    139m24.408s

    cat fb.galGal6.chainRBest.Hg38.txt
    # 106294585 bases of 1055588482 (10.070%) in intersection

#############################################################################
# LASTZ Cow bosTau9 (DONE - 2018-11-08 - Hiram)
    mkdir /hive/data/genomes/hg38/bed/lastzBosTau9.2018-11-08
    cd /hive/data/genomes/hg38/bed/lastzBosTau9.2018-11-08

    printf '# human vs Cow
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.00/bin/lastz
BLASTZ_T=2
BLASTZ_O=400
BLASTZ_E=30
BLASTZ_M=254
# default BLASTZ_Q score matrix:
#       A     C     G     T
# A    91  -114   -31  -123
# C  -114   100  -125   -31
# G   -31  -125   100  -114
# T  -123   -31  -114    91

# TARGET: human hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CTGDIR=/hive/data/genomes/hg38/hg38.contigs.2bit
SEQ1_CTGLEN=/hive/data/genomes/hg38/hg38.contigs.chrom.sizes
SEQ1_LIFT=/hive/data/genomes/hg38/jkStuff/hg38.contigs.lift
SEQ1_CHUNK=40000000
SEQ1_LIMIT=5
SEQ1_LAP=10000

# QUERY: Cow bosTau9
SEQ2_DIR=/hive/data/genomes/bosTau9/bosTau9.2bit
SEQ2_LEN=/hive/data/genomes/bosTau9/chrom.sizes
SEQ2_CHUNK=20000000
SEQ2_LIMIT=10
SEQ2_LAP=0

BASE=/hive/data/genomes/hg38/bed/lastzBosTau9.2018-11-08
TMPDIR=/dev/shm
' > DEF

    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
        -chainMinScore=3000 -chainLinearGap=medium \
          -workhorse=hgwdev -smallClusterHub=hgwdev-101 -bigClusterHub=ku \
            -syntenicNet) > do.log 2>&1
    # real    393m17.228s

    cat fb.hg38.chainBosTau9Link.txt
    # 1402568450 bases of 3095998939 (45.303%) in intersection
    cat fb.hg38.chainSynBosTau9Link.txt
    # 1345897937 bases of 3095998939 (43.472%) in intersection

    time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` hg38 bosTau9) > rbest.log 2>&1 &
    #	real    273m2.085s

    cat fb.hg38.chainRBest.BosTau9.txt
    #	1290064468 bases of 3095998939 (41.669%) in intersection

    #   running the swap
    mkdir /hive/data/genomes/bosTau9/bed/blastz.hg38.swap
    cd /hive/data/genomes/bosTau9/bed/blastz.hg38.swap
    time (doBlastzChainNet.pl -verbose=2 \
        /hive/data/genomes/hg38/bed/lastzBosTau9.2018-11-08/DEF \
        -swap  -syntenicNet -workhorse=hgwdev \
	-smallClusterHub=hgwdev-101 -bigClusterHub=ku \
        -chainMinScore=3000 -chainLinearGap=medium) > swap.log 2>&1
    #   real    69m11.226s

    cat fb.bosTau9.chainHg38Link.txt
    #   1342860432 bases of 2715853792 (49.445%) in intersection
    cat fb.bosTau9.chainSynHg38Link.txt
    #	1306095676 bases of 2715853792 (48.092%) in intersection

    time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` bosTau9 hg38) > rbest.log 2>&1 &
    # real    272m15.176s

    cat fb.bosTau9.chainRBest.Hg38.txt
    # 1290810412 bases of 2715853792 (47.529%) in intersection

#############################################################################
# LASTZ human/hg38 vs. Japanese quail/cotJap2 - (DONE - 2018-11-15 - Hiram)
    mkdir /hive/data/genomes/hg38/bed/lastzCotJap2.2018-11-15
    cd /hive/data/genomes/hg38/bed/lastzCotJap2.2018-11-15

    printf "# human vs Japanese quail
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.00/bin/lastz
BLASTZ_O=400
BLASTZ_E=30
BLASTZ_Y=3400
BLASTZ_L=6000
BLASTZ_K=2200
BLASTZ_M=50
BLASTZ_Q=/scratch/data/blastz/HoxD55.q
#      A    C    G    T
#     91  -90  -25 -100
#    -90  100 -100  -25
#    -25 -100  100  -90
#   -100  -25  -90  91

# TARGET: human hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CTGDIR=/hive/data/genomes/hg38/hg38.contigs.2bit
SEQ1_CTGLEN=/hive/data/genomes/hg38/hg38.contigs.chrom.sizes
SEQ1_LIFT=/hive/data/genomes/hg38/jkStuff/hg38.contigs.lift
SEQ1_CHUNK=40000000
SEQ1_LIMIT=30
SEQ1_LAP=10000

# QUERY: Japanese quail cotJap2
SEQ2_DIR=/hive/data/genomes/cotJap2/cotJap2.2bit
SEQ2_LEN=/hive/data/genomes/cotJap2/chrom.sizes
SEQ2_CHUNK=20000000
SEQ2_LIMIT=30
SEQ2_LAP=0

BASE=/hive/data/genomes/hg38/bed/lastzCotJap2.2018-11-15
TMPDIR=/dev/shm
" > DEF

    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
        -chainMinScore=5000 -chainLinearGap=loose \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > do.log 2>&1
    # real    81m22.929s

    cat fb.hg38.chainCotJap2Link.txt
    # 139668231 bases of 3095998939 (4.511%) in intersection

    cat fb.hg38.chainSynCotJap2Link.txt
    # 90319008 bases of 3095998939 (2.917%) in intersection

    time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` hg38 cotJap2) > rbest.log 2>&1 &
    # real    136m44.926s

    cat fb.hg38.chainRBest.CotJap2.txt
    # 99806762 bases of 3095998939 (3.224%) in intersection

    # and for the swap:
    mkdir /hive/data/genomes/cotJap2/bed/blastz.hg38.swap
    cd /hive/data/genomes/cotJap2/bed/blastz.hg38.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/hg38/bed/lastzCotJap2.2018-11-15/DEF \
        -swap -chainMinScore=5000 -chainLinearGap=loose \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    #  real    8m9.892s

    cat fb.cotJap2.chainHg38Link.txt
    # 108800437 bases of 917263224 (11.861%) in intersection
    cat fb.cotJap2.chainSynHg38Link.txt
    # 87569432 bases of 917263224 (9.547%) in intersection

    # mistakenly started this on ku, it failed at the download step since
    # it could not see the /gbdb/mm10/ hierarchy:
    time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` cotJap2 hg38) > rbest.log 2>&1 &
    # real    99m33.362s

    # continue on hgwdev
    time (doRecipBest.pl -load -workhorse=hgwdev -continue=download -buildDir=`pwd` cotJap2 hg38) > rbest.download.log 2>&1 &
    # real    1m53.130s

    cat fb.cotJap2.chainRBest.Hg38.txt
    # 99417593 bases of 917263224 (10.839%) in intersection

#############################################################################
# LASTZ human/hg38 mouse/GRCm38B - (DONE - 2019-03-01 - Hiram)
    mkdir /hive/data/genomes/hg38/bed/lastzGRCm38B.2019-03-01
    cd /hive/data/genomes/hg38/bed/lastzGRCm38B.2019-03-01

    printf '# human vs mouse
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.00/bin/lastz

# TARGET: Human Hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CTGDIR=/hive/data/genomes/hg38/hg38.contigs.2bit
SEQ1_CTGLEN=/hive/data/genomes/hg38/hg38.contigs.chrom.sizes
SEQ1_LIFT=/hive/data/genomes/hg38/jkStuff/hg38.contigs.lift
SEQ1_CHUNK=40000000
SEQ1_LAP=10000

# QUERY: Mouse GRCm38B
SEQ2_DIR=/hive/data/genomes/GRCm38B/GRCm38B.2bit
SEQ2_LEN=/hive/data/genomes/GRCm38B/chrom.sizes
SEQ2_CHUNK=20000000
SEQ2_LAP=0

BASE=/hive/data/genomes/hg38/bed/lastzGRCm38B.2019-03-01
TMPDIR=/dev/shm
' > DEF

    time (doBlastzChainNet.pl -verbose=2 `pwd`/DEF -noDbNameCheck \
        -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev-101 \
	 -fileServer=hgwdev \
        -bigClusterHub=ku -chainMinScore=3000 -chainLinearGap=medium) \
           > do.log 2>&1
    # real    171m59.392s

    cat fb.hg38.chainGRCm38BLink.txt
    # 967404497 bases of 3095998939 (31.247%) in intersection
    cat fb.hg38.chainSynGRCm38BLink.txt
    # 913717211 bases of 3095998939 (29.513%) in intersection

    time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` hg38 GRCm38B) \
     > rbest.log 2>&1 &
    # real    284m45.623s

    cat fb.hg38.chainRBest.GRCm38B.txt
    # 891970056 bases of 3095998939 (28.810%) in intersection

    # and for the swap:
    mkdir /hive/data/genomes/GRCm38B/bed/blastz.hg38.swap
    cd /hive/data/genomes/GRCm38B/bed/blastz.hg38.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/hg38/bed/lastzGRCm38B.2019-03-01/DEF \
        -swap -chainMinScore=3000 -chainLinearGap=medium \
          -workhorse=hgwdev -smallClusterHub=hgwdev-101 -bigClusterHub=ku \
            -noDbNameCheck -syntenicNet) > swap.log 2>&1
    #  real    60m31.849s

    cat fb.GRCm38B.chainHg38Link.txt
    # 941205213 bases of 2655285420 (35.446%) in intersection
    cat fb.GRCm38B.chainSynHg38Link.txt
    # 891450770 bases of 2655285420 (33.573%) in intersection

    time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` GRCm38B hg38) \
     > rbest.log 2>&1 &
    # real    331m35.578s

    cat fb.GRCm38B.chainRBest.Hg38.txt
    # 893587236 bases of 2655285420 (33.653%) in intersection

#########################################################################
# LASTZ human/hg38 vs. rat/regenRn0 - (DONE - 2019-07-01 - Hiram)
    mkdir /hive/data/genomes/hg38/bed/lastzRegenRn0.2019-07-01
    cd /hive/data/genomes/hg38/bed/lastzRegenRn0.2019-07-01

    printf '# human vs rat
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.00/bin/lastz

# TARGET: human hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CTGDIR=/hive/data/genomes/hg38/hg38.contigs.2bit
SEQ1_CTGLEN=/hive/data/genomes/hg38/hg38.contigs.chrom.sizes
SEQ1_LIFT=/hive/data/genomes/hg38/jkStuff/hg38.contigs.lift
SEQ1_CHUNK=40000000
SEQ1_LIMIT=30
SEQ1_LAP=10000

# QUERY: rat regenRn0
SEQ2_DIR=/hive/data/genomes/regenRn0/regenRn0.2bit
SEQ2_LEN=/hive/data/genomes/regenRn0/chrom.sizes
SEQ2_CHUNK=20000000
SEQ2_LIMIT=30
SEQ2_LAP=0

BASE=/hive/data/genomes/hg38/bed/lastzRegenRn0.2019-07-01
TMPDIR=/dev/shm
' > DEF

    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
        -chainMinScore=3000 -chainLinearGap=medium -noDbNameCheck \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > do.log 2>&1 &
    # real    256m8.479s

    cat fb.hg38.chainRegenRn0Link.txt
    # 930788096 bases of 3095998939 (30.064%) in intersection
    cat fb.hg38.chainSynRegenRn0Link.txt
    # 870556908 bases of 3095998939 (28.119%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -load -buildDir=`pwd` hg38 regenRn0) > rbest.log 2>&1 &
    # real    328m4.069s

    cat fb.hg38.chainRBest.RegenRn0.txt
    # 857127621 bases of 3095998939 (27.685%) in intersection

    # and for the swap:
    mkdir /hive/data/genomes/regenRn0/bed/blastz.hg38.swap
    cd /hive/data/genomes/regenRn0/bed/blastz.hg38.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/hg38/bed/lastzRegenRn0.2019-07-01/DEF \
        -swap -chainMinScore=3000 -chainLinearGap=medium -noDbNameCheck \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    #  real    64m34.515s

    cat fb.regenRn0.chainHg38Link.txt
    # 906790361 bases of 2534810853 (35.773%) in intersection
    cat fb.regenRn0.chainSynHg38Link.txt
    # 849997639 bases of 2534810853 (33.533%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -load -buildDir=`pwd` regenRn0 hg38) > rbest.log 2>&1
    # real    300m30.411s

    cat fb.regenRn0.chainRBest.Hg38.txt
    # 858923025 bases of 2534810853 (33.885%) in intersection

#########################################################################
# LASTZ human/hg38 Tree chimp/rheMac10 - (DONE - 2019-07-03 - Hiram)
    mkdir /hive/data/genomes/hg38/bed/lastzRheMac10.2019-07-03
    cd /hive/data/genomes/hg38/bed/lastzRheMac10.2019-07-03

    printf '# human vs macaca mulatta
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.00/bin/lastz
# maximum M allowed with lastz is only 254
BLASTZ_M=254
BLASTZ_Q=/hive/data/staging/data/blastz/human_chimp.v2.q
BLASTZ_O=600
BLASTZ_E=150
# other parameters from panTro2 vs hg18 lastz on advice from Webb
BLASTZ_K=4500
BLASTZ_Y=15000
BLASTZ_T=2

# TARGET: Human Hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CTGDIR=/hive/data/genomes/hg38/hg38.contigs.2bit
SEQ1_CTGLEN=/hive/data/genomes/hg38/hg38.contigs.chrom.sizes
SEQ1_LIFT=/hive/data/genomes/hg38/jkStuff/hg38.contigs.lift
SEQ1_CHUNK=20000000
SEQ1_LAP=10000

# QUERY: Macaca Mulatta RheMac10
SEQ2_DIR=/hive/data/genomes/rheMac10/rheMac10.2bit
SEQ2_LEN=/hive/data/genomes/rheMac10/chrom.sizes
SEQ2_CHUNK=20000000
SEQ2_LIMIT=600
SEQ2_LAP=0
SEQ2_IN_CONTIGS=0

BASE=/hive/data/genomes/hg38/bed/lastzRheMac10.2019-07-03
TMPDIR=/dev/shm
' > DEF
    # << happy emacs

    time (doBlastzChainNet.pl -verbose=2 `pwd`/DEF \
        -syntenicNet -fileServer=hgwdev \
        -chainMinScore=5000 -chainLinearGap=medium \
        -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku) > do.log 2>&1
    # real    97m36.383s

    cat fb.hg38.chainRheMac10Link.txt
    # 2596157811 bases of 3095998939 (83.855%) in intersection
    cat fb.hg38.chainSynRheMac10Link.txt
    # 2564291936 bases of 3095998939 (82.826%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -load -buildDir=`pwd` hg38 rheMac10) > rbest.log 2>&1 &
    # real    120m8.526s

    cat fb.hg38.chainRBest.RheMac10.txt
    # 2422981614 bases of 3095998939 (78.262%) in intersection

    # and for the swap:
    mkdir /hive/data/genomes/rheMac10/bed/blastz.hg38.swap
    cd /hive/data/genomes/rheMac10/bed/blastz.hg38.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/hg38/bed/lastzRheMac10.2019-07-03/DEF \
        -swap -chainMinScore=5000 -chainLinearGap=medium \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    #  real    61m39.505s

    cat fb.rheMac10.chainHg38Link.txt
    # 2485840115 bases of 2936892733 (84.642%) in intersection
    cat fb.rheMac10.chainSynHg38Link.txt
    # 2465210442 bases of 2936892733 (83.939%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -load -buildDir=`pwd` rheMac10 hg38) > rbest.log 2>&1
    # real    126m29.919s

    cat fb.rheMac10.chainRBest.Hg38.txt
    # 2424028492 bases of 2936892733 (82.537%) in intersection

#########################################################################
# LASTZ human/hg38 vs. rat/regenRn1 - (DONE - 2019-09-12 - Hiram)
    mkdir /hive/data/genomes/hg38/bed/lastzRegenRn1.2019-09-12
    cd /hive/data/genomes/hg38/bed/lastzRegenRn1.2019-09-12

    printf '# human vs rat
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.00/bin/lastz

# TARGET: human hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CTGDIR=/hive/data/genomes/hg38/hg38.contigs.2bit
SEQ1_CTGLEN=/hive/data/genomes/hg38/hg38.contigs.chrom.sizes
SEQ1_LIFT=/hive/data/genomes/hg38/jkStuff/hg38.contigs.lift
SEQ1_CHUNK=40000000
SEQ1_LIMIT=30
SEQ1_LAP=10000

# QUERY: rat regenRn1
SEQ2_DIR=/hive/data/genomes/regenRn1/regenRn1.2bit
SEQ2_LEN=/hive/data/genomes/regenRn1/chrom.sizes
SEQ2_CHUNK=20000000
SEQ2_LIMIT=30
SEQ2_LAP=0

BASE=/hive/data/genomes/hg38/bed/lastzRegenRn1.2019-09-12
TMPDIR=/dev/shm
' > DEF

    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
        -chainMinScore=3000 -chainLinearGap=medium -noDbNameCheck \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > do.log 2>&1 &
    # real    162m40.237s

    cat fb.hg38.chainRegenRn1Link.txt
    # 863041482 bases of 3095998939 (27.876%) in intersection
    cat fb.hg38.chainSynRegenRn1Link.txt
    # 809332351 bases of 3095998939 (26.141%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -load -buildDir=`pwd` hg38 regenRn1) > rbest.log 2>&1 &
    # real    261m19.645s

    cat fb.hg38.chainRBest.RegenRn1.txt
    # 792532873 bases of 3095998939 (25.599%) in intersection

    # and for the swap:
    mkdir /hive/data/genomes/regenRn1/bed/blastz.hg38.swap
    cd /hive/data/genomes/regenRn1/bed/blastz.hg38.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/hg38/bed/lastzRegenRn1.2019-09-12/DEF \
        -swap -chainMinScore=3000 -chainLinearGap=medium -noDbNameCheck \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    #  real    63m47.773s

    cat fb.regenRn1.chainHg38Link.txt
    # 827167139 bases of 2282482188 (36.240%) in intersection
    cat fb.regenRn1.chainSynHg38Link.txt
    # 788025130 bases of 2282482188 (34.525%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -load -buildDir=`pwd` regenRn1 hg38) > rbest.log 2>&1
    # real    300m50.570s

    cat fb.regenRn1.chainRBest.Hg38.txt
    # 793987134 bases of 2282482188 (34.786%) in intersection

#########################################################################
# LASTZ human/hg38 Gorilla/gorGor6 - (DONE - 2019-11-20 - Hiram)
    mkdir /hive/data/genomes/hg38/bed/lastzGorGor6.2019-11-20
    cd /hive/data/genomes/hg38/bed/lastzGorGor6.2019-11-20

    printf '# human vs gorilla
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.00/bin/lastz
BLASTZ_T=2
BLASTZ_O=600
BLASTZ_E=150
BLASTZ_M=254
BLASTZ_K=4500
BLASTZ_Y=15000
BLASTZ_Q=/hive/data/staging/data/blastz/human_chimp.v2.q
#       A     C     G     T
# A    90  -330  -236  -356
# C  -330   100  -318  -236
# G  -236  -318   100  -330
# T  -356  -236  -330    90

# TARGET: human hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
SEQ1_IN_CONTIGS=0

# QUERY: gorilla gorGor6
SEQ2_DIR=/hive/data/genomes/gorGor6/gorGor6.2bit
SEQ2_LEN=/hive/data/genomes/gorGor6/chrom.sizes
SEQ2_CHUNK=20000000
SEQ2_LAP=0
SEQ2_LIMIT=50

BASE=/hive/data/genomes/hg38/bed/lastzGorGor6.2019-11-20
TMPDIR=/dev/shm
' > DEF

    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
        -chainMinScore=3000 -chainLinearGap=medium \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > do.log 2>&1
    # broken cluster run due to path name for BLASTZ_Q, continuing:
    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
        -chainMinScore=3000 -chainLinearGap=medium \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -continue=cat -syntenicNet) > cat.log 2>&1
    # real    77m19.538s

    cat fb.hg38.chainGorGor6Link.txt
    # 2908900659 bases of 3095998939 (93.957%) in intersection
    cat fb.hg38.chainSynGorGor6Link.txt
    # 2885980361 bases of 3095998939 (93.216%) in intersection

    time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` hg38 gorGor6) \
        > rbest.log 2>&1 &
    # real    65m39.724s

    cat fb.hg38.chainRBest.GorGor6.txt
    # 2693876207 bases of 3095998939 (87.012%) in intersection

    # and for the swap:
    mkdir /hive/data/genomes/gorGor6/bed/blastz.hg38.swap
    cd /hive/data/genomes/gorGor6/bed/blastz.hg38.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/hg38/bed/lastzGorGor6.2019-11-20/DEF \
        -swap -chainMinScore=3000 -chainLinearGap=medium \
          -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    #  real    63m46.473s

    cat fb.gorGor6.chainHg38Link.txt
    # 2738870921 bases of 2999027915 (91.325%) in intersection
    cat fb.gorGor6.chainSynHg38Link.txt
    # 2728591501 bases of 2999027915 (90.983%) in intersection

    time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` gorGor6 hg38) \
       > rbest.log 2>&1
    # real    62m14.470s

    cat fb.gorGor6.chainRBest.Hg38.txt
    # 2697792568 bases of 2999027915 (89.956%) in intersection

#############################################################################
# LASTZ human/hg38 vs. Chinese hamster CHO-K1 cell line/regenCho1
#	(DONE - 2019-11-26 - Hiram)

    mkdir /hive/data/genomes/hg38/bed/lastzRegenCho1.2019-11-26
    cd /hive/data/genomes/hg38/bed/lastzRegenCho1.2019-11-26

    printf '# human vs Chinese hamster ovary CHO-K1 cell line
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.00/bin/lastz
BLASTZ_M=254

# TARGET: human hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CTGDIR=/hive/data/genomes/hg38/hg38.contigs.2bit
SEQ1_CTGLEN=/hive/data/genomes/hg38/hg38.contigs.chrom.sizes
SEQ1_LIFT=/hive/data/genomes/hg38/jkStuff/hg38.contigs.lift
SEQ1_CHUNK=40000000
SEQ1_LIMIT=20
SEQ1_LAP=10000

# QUERY: Chinese hamster ovary CHO-K1 cell line regenCho1
SEQ2_DIR=/hive/data/genomes/regenCho1/regenCho1.2bit
SEQ2_LEN=/hive/data/genomes/regenCho1/chrom.sizes
SEQ2_CHUNK=20000000
SEQ2_LIMIT=20
SEQ2_LAP=0

BASE=/hive/data/genomes/hg38/bed/lastzRegenCho1.2019-11-26
TMPDIR=/dev/shm
' > DEF

    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
        -chainMinScore=3000 -chainLinearGap=medium \
          -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
            -noDbNameCheck -syntenicNet) > do.log 2>&1
    # real    376m47.828s

    cat fb.hg38.chainRegenCho1Link.txt
    # 979733899 bases of 3095998939 (31.645%) in intersection
    cat fb.hg38.chainSynRegenCho1Link.txt
    # 917104031 bases of 3095998939 (29.622%) in intersection

    time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \
	hg38 regenCho1) > rbest.log 2>&1 &
    # real    259m42.688s

    cat fb.hg38.chainRBest.RegenCho1.txt
    # 901006295 bases of 3095998939 (29.102%) in intersection

    # and for the swap:
    mkdir /hive/data/genomes/regenCho1/bed/blastz.hg38.swap
    cd /hive/data/genomes/regenCho1/bed/blastz.hg38.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/hg38/bed/lastzRegenCho1.2019-11-26/DEF \
        -swap -chainMinScore=3000 -chainLinearGap=medium \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -noDbNameCheck -syntenicNet) > swap.log 2>&1
    #  real    79m18.904s

    cat fb.regenCho1.chainHg38Link.txt
    # 956720146 bases of 2266312740 (42.215%) in intersection
    cat fb.regenCho1.chainSynHg38Link.txt
    # 895755077 bases of 2266312740 (39.525%) in intersection

    time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \
	regenCho1 hg38) > rbest.log 2>&1 &
    # real    289m24.440s

    cat fb.regenCho1.chainRBest.Hg38.txt
    # 902782523 bases of 2266312740 (39.835%) in intersection

#############################################################################
# LASTZ human/hg38 vs. Southern Sea Otter/enhLutNer1
#	(DONE - 2019-12-22 - Jonathan)

    mkdir /hive/data/genomes/hg38/bed/lastzEnhLutNer1.2019-12-20
    cd /hive/data/genomes/hg38/bed/lastzEnhLutNer1.2019-12-20

    printf '# human vs Southern sea otter
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.00/bin/lastz
BLASTZ_M=254

# TARGET: human hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CTGDIR=/hive/data/genomes/hg38/hg38.contigs.2bit
SEQ1_CTGLEN=/hive/data/genomes/hg38/hg38.contigs.chrom.sizes
SEQ1_LIFT=/hive/data/genomes/hg38/jkStuff/hg38.contigs.lift
SEQ1_CHUNK=40000000
SEQ1_LIMIT=20
SEQ1_LAP=10000

# QUERY: Southern sea otter enhLutNer1
SEQ2_DIR=/hive/data/genomes/enhLutNer1/enhLutNer1.2bit
SEQ2_LEN=/hive/data/genomes/enhLutNer1/chrom.sizes
SEQ2_CHUNK=20000000
SEQ2_LIMIT=20
SEQ2_LAP=0

BASE=/hive/data/genomes/hg38/bed/lastzEnhLutNer1.2019-12-20
TMPDIR=/dev/shm
' > DEF

    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
        -chainMinScore=3000 -chainLinearGap=medium \
          -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
            -noDbNameCheck -syntenicNet) > do.log 2>&1
    # real    336m47.917s

    cat fb.hg38.chainEnhLutNer1Link.txt
    # 1537745313 bases of 3095998939 (49.669%) in intersection
    cat fb.hg38.chainSynEnhLutNer1Link.txt
    # 1454400074 bases of 3095998939 (46.977%) in intersection

    time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \
	hg38 enhLutNer1) > rbest.log 2>&1 &
    # real    336m47.917s

    cat fb.hg38.chainRBest.EnhLutNer1.txt
    # 1413203552 bases of 3095998939 (45.646%) in intersection

    # and for the swap:
    mkdir /hive/data/genomes/enhLutNer1/bed/blastz.hg38.swap
    cd /hive/data/genomes/enhLutNer1/bed/blastz.hg38.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/hg38/bed/lastzEnhLutNer1.2019-12-20/DEF \
        -swap -chainMinScore=3000 -chainLinearGap=medium \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -noDbNameCheck -syntenicNet) > swap.log 2>&1
    #  real    88m38.087s

    cat fb.enhLutNer1.chainHg38Link.txt
    # 1526639908 bases of 2413653822 (63.250%) in intersection
    cat fb.enhLutNer1.chainSynHg38Link.txt
    # 1403546142 bases of 2413653822 (58.150%) in intersection

    time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \
	enhLutNer1 hg38) > rbest.log 2>&1 &
    # real    319m54.030s

    cat fb.enhLutNer1.chainRBest.Hg38.txt
    # 1414347523 bases of 2413653822 (58.598%) in intersection

#########################################################################
# LASTZ human/hg38 vs. German shepard/canFam4
#	(DONE - 2020-04-02 - Hiram)

    mkdir /hive/data/genomes/hg38/bed/lastzCanFam4.2020-04-02
    cd /hive/data/genomes/hg38/bed/lastzCanFam4.2020-04-02

    printf '# human vs. German shepard
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz
BLASTZ_M=254

# TARGET: human hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CTGDIR=/hive/data/genomes/hg38/hg38.contigs.2bit
SEQ1_CTGLEN=/hive/data/genomes/hg38/hg38.contigs.chrom.sizes
SEQ1_LIFT=/hive/data/genomes/hg38/jkStuff/hg38.contigs.lift
SEQ1_CHUNK=40000000
SEQ1_LIMIT=20
SEQ1_LAP=10000

# QUERY: German shepard Mischka/canFam4
SEQ2_DIR=/hive/data/genomes/canFam4/canFam4.2bit
SEQ2_LEN=/hive/data/genomes/canFam4/chrom.sizes
SEQ2_CHUNK=20000000
SEQ2_LIMIT=20
SEQ2_LAP=0

BASE=/hive/data/genomes/hg38/bed/lastzCanFam4.2020-04-02
TMPDIR=/dev/shm
' > DEF

    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
        -chainMinScore=3000 -chainLinearGap=medium \
          -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
            -syntenicNet) > do.log 2>&1
    # real    904m29.420s

    cat fb.hg38.chainCanFam4Link.txt
    # 1549397508 bases of 3110768607 (49.808%) in intersection
    cat fb.hg38.chainSynCanFam4Link.txt
    # 1488468205 bases of 3110768607 (47.849%) in intersection

    time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \
	hg38 canFam4) > rbest.log 2>&1 &
    # real    310m32.196s

    cat fb.hg38.chainRBest.CanFam4.txt
    # 1425406620 bases of 3110768607 (45.822%) in intersection

    # and for the swap:
    mkdir /hive/data/genomes/canFam4/bed/blastz.hg38.swap
    cd /hive/data/genomes/canFam4/bed/blastz.hg38.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/hg38/bed/lastzCanFam4.2020-04-02/DEF \
        -swap -chainMinScore=3000 -chainLinearGap=medium \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    #  real    99m10.990s

    cat fb.canFam4.chainHg38Link.txt
    # 1493209286 bases of 2481941580 (60.163%) in intersection
    cat fb.canFam4.chainSynHg38Link.txt
    # 1448164376 bases of 2481941580 (58.348%) in intersection

    time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \
	canFam4 hg38) > rbest.log 2>&1 &
    # real    257m59.713s

    cat fb.canFam4.chainRBest.Hg38.txt
    # 1425296830 bases of 2481941580 (57.427%) in intersection

#########################################################################
# LASTZ human/hg38 bonobo/panPan3 - (DONE - 2020-06-15 - Hiram)
    mkdir /hive/data/genomes/hg38/bed/lastzPanPan3.2020-06-15
    cd /hive/data/genomes/hg38/bed/lastzPanPan3.2020-06-15

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

# TARGET: human hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CTGDIR=/hive/data/genomes/hg38/hg38.contigs.2bit
SEQ1_CTGLEN=/hive/data/genomes/hg38/hg38.contigs.chrom.sizes
SEQ1_LIFT=/hive/data/genomes/hg38/jkStuff/hg38.contigs.lift
SEQ1_CHUNK=40000000
SEQ1_LIMIT=10
SEQ1_LAP=10000

# QUERY: bonobo panPan3
SEQ2_DIR=/hive/data/genomes/panPan3/panPan3.2bit
SEQ2_LEN=/hive/data/genomes/panPan3/chrom.sizes
SEQ2_CHUNK=20000000
SEQ2_LIMIT=50
SEQ2_LAP=0

BASE=/hive/data/genomes/hg38/bed/lastzPanPan3.2020-06-15
TMPDIR=/dev/shm
' > DEF

    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
        -chainMinScore=3000 -chainLinearGap=medium \
          -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
            -syntenicNet) > do.log 2>&1
    # real    117m56.403s

    cat fb.hg38.chainPanPan3Link.txt
    # 2897225010 bases of 3110768607 (93.135%) in intersection

    cat fb.hg38.chainSynPanPan3Link.txt
    # 2880116277 bases of 3110768607 (92.585%) in intersection

    time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \
	hg38 panPan3) > rbest.log 2>&1 &
    # real    68m45.187s
    cat fb.hg38.chainRBest.PanPan3.txt
    # 2727319248 bases of 3110768607 (87.673%) in intersection

    # and for the swap:
    mkdir /hive/data/genomes/panPan3/bed/blastz.hg38.swap
    cd /hive/data/genomes/panPan3/bed/blastz.hg38.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/hg38/bed/lastzPanPan3.2020-06-15/DEF \
        -swap -chainMinScore=3000 -chainLinearGap=medium \
          -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    #  real    73m50.456s

    cat fb.panPan3.chainHg38Link.txt
    # 2777869191 bases of 3015350297 (92.124%) in intersection
    cat fb.panPan3.chainSynHg38Link.txt
    # 2768018012 bases of 3015350297 (91.798%) in intersection

    time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \
      panPan3 hg38) > rbest.log 2>&1 &
    # real    66m52.340s
    cat fb.panPan3.chainRBest.Hg38.txt
    # 2732415393 bases of 3015350297 (90.617%) in intersection

#########################################################################
# LASTZ human/hg38 vs. Great Dane/canFam5
#	(DONE - 2020-07-29 - Hiram)

    mkdir /hive/data/genomes/hg38/bed/lastzCanFam5.2020-07-29
    cd /hive/data/genomes/hg38/bed/lastzCanFam5.2020-07-29

    printf '# human vs. Great Dane
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz
BLASTZ_M=254

# TARGET: human hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CTGDIR=/hive/data/genomes/hg38/hg38.contigs.2bit
SEQ1_CTGLEN=/hive/data/genomes/hg38/hg38.contigs.chrom.sizes
SEQ1_LIFT=/hive/data/genomes/hg38/jkStuff/hg38.contigs.lift
SEQ1_CHUNK=40000000
SEQ1_LIMIT=20
SEQ1_LAP=10000

# QUERY: Great Dane Zoey/canFam5
SEQ2_DIR=/hive/data/genomes/canFam5/canFam5.2bit
SEQ2_LEN=/hive/data/genomes/canFam5/chrom.sizes
SEQ2_CHUNK=20000000
SEQ2_LIMIT=20
SEQ2_LAP=0

BASE=/hive/data/genomes/hg38/bed/lastzCanFam5.2020-07-29
TMPDIR=/dev/shm
' > DEF

    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
        -chainMinScore=3000 -chainLinearGap=medium \
          -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
            -syntenicNet) > do.log 2>&1
    # real    1038m20.721s

    cat fb.hg38.chainCanFam5Link.txt
    # 1545648756 bases of 3110768607 (49.687%) in intersection

    cat fb.hg38.chainSynCanFam5Link.txt
    # 1484758745 bases of 3110768607 (47.730%) in intersection

    time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \
	hg38 canFam5) > rbest.log 2>&1 &
    # real    283m55.399s

    cat fb.hg38.chainRBest.CanFam5.txt
    # 1422619513 bases of 3110768607 (45.732%) in intersection

    # and for the swap:
    mkdir /hive/data/genomes/canFam5/bed/blastz.hg38.swap
    cd /hive/data/genomes/canFam5/bed/blastz.hg38.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/hg38/bed/lastzCanFam5.2020-07-29/DEF \
        -swap -chainMinScore=3000 -chainLinearGap=medium \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    #  real    78m37.078s

    cat fb.canFam5.chainHg38Link.txt
    # 1460025525 bases of 2337131234 (62.471%) in intersection
    cat fb.canFam5.chainSynHg38Link.txt
    # 1423305734 bases of 2337131234 (60.900%) in intersection

    time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \
	canFam5 hg38) > rbest.log 2>&1 &
    # real    255m9.076s

    cat fb.canFam5.chainRBest.Hg38.txt
    # 1422612399 bases of 2337131234 (60.870%) in intersection

############################################################################
# LASTZ MOUSE Mm39 (DONE - 2020-08-17 - Hiram)
    # can no longer use the lineage specific repeats with the new lastz
    # use a screen to manage this longish job:
    screen -S hg38Mm39

    mkdir /hive/data/genomes/hg38/bed/lastzMm39.2020-08-17
    cd /hive/data/genomes/hg38/bed/lastzMm39.2020-08-17

    # best to always specify an exact path to lastz so we know which one is used
    # lastz default parameters are human-mouse parameters

    printf '# human vs mouse
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz

# TARGET: Human Hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CTGDIR=/hive/data/genomes/hg38/hg38.contigs.2bit
SEQ1_CTGLEN=/hive/data/genomes/hg38/hg38.contigs.chrom.sizes
SEQ1_LIFT=/hive/data/genomes/hg38/jkStuff/hg38.contigs.lift
SEQ1_CHUNK=40000000
SEQ1_LAP=10000

# QUERY: Mouse Mm39
SEQ2_DIR=/hive/data/genomes/mm39/mm39.2bit
SEQ2_LEN=/hive/data/genomes/mm39/chrom.sizes
SEQ2_CHUNK=20000000
SEQ2_LAP=0

BASE=/hive/data/genomes/hg38/bed/lastzMm39.2020-08-17
TMPDIR=/dev/shm
' > DEF

    # verify files exist:
    grep "=" DEF | cut -d= -f2 | xargs ls -ogd

    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
        -chainMinScore=3000 -chainLinearGap=medium \
          -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
            -syntenicNet) > do.log 2>&1
    # real    209m17.257s

    sed -e 's/^/    # /;' fb.hg38.chainMm39Link.txt
    # 966592868 bases of 3110768607 (31.072%) in intersection

    sed -e 's/^/    # /;' fb.hg38.chainSynMm39Link.txt
    # 913448433 bases of 3110768607 (29.364%) in intersection

    time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \
	hg38 mm39) > rbest.log 2>&1 &
    # real    267m52.694s

    sed -e 's/^/    # /;' fb.hg38.chainRBest.Mm39.txt
    # 891660271 bases of 3110768607 (28.664%) in intersection

    #	and the swap
    mkdir /hive/data/genomes/mm39/bed/blastz.hg38.swap
    cd /hive/data/genomes/mm39/bed/blastz.hg38.swap
    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/hg38/bed/lastzMm39.2020-08-17/DEF \
        -chainMinScore=3000 -chainLinearGap=medium \
          -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
            -swap -syntenicNet) > swap.log 2>&1
    #   real    47m57.164s

    sed -e 's/^/    # /;' fb.mm39.chainHg38Link.txt
    # 939000954 bases of 2654624157 (35.372%) in intersection
    sed -e 's/^/    # /;' fb.mm39.chainSynHg38Link.txt
    # 891050480 bases of 2654624157 (33.566%) in intersection

    time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \
	mm39 hg38) > rbest.log 2>&1 &
    # real    257m59.713s

    sed -e 's/^/    # /;' fb.mm39.chainRBest.Hg38.txt
    # 893176796 bases of 2654624157 (33.646%) in intersection

#########################################################################
# LASTZ human/hg38 vs. marmoset/calJac4
#	(DONE - 2020-08-03.g - Hiram)

    mkdir /hive/data/genomes/hg38/bed/lastzCalJac4.2020-08-03
    cd /hive/data/genomes/hg38/bed/lastzCalJac4.2020-08-03

    printf '# human vs. marmoset
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz
BLASTZ_M=254

# TARGET: human hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CTGDIR=/hive/data/genomes/hg38/hg38.contigs.2bit
SEQ1_CTGLEN=/hive/data/genomes/hg38/hg38.contigs.chrom.sizes
SEQ1_LIFT=/hive/data/genomes/hg38/jkStuff/hg38.contigs.lift
SEQ1_CHUNK=40000000
SEQ1_LIMIT=20
SEQ1_LAP=10000

# QUERY: marmoset/calJac4
SEQ2_DIR=/hive/data/genomes/calJac4/calJac4.2bit
SEQ2_LEN=/hive/data/genomes/calJac4/chrom.sizes
SEQ2_CHUNK=20000000
SEQ2_LIMIT=20
SEQ2_LAP=0

BASE=/hive/data/genomes/hg38/bed/lastzCalJac4.2020-08-03
TMPDIR=/dev/shm
' > DEF

    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
        -chainMinScore=3000 -chainLinearGap=medium \
          -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
            -syntenicNet) > do.log 2>&1
    # real    560m59.358s

    cat fb.hg38.chainCalJac4Link.txt
    # 2338614467 bases of 3110768607 (75.178%) in intersection

    cat fb.hg38.chainSynCalJac4Link.txt
    # 2261509186 bases of 3110768607 (72.699%) in intersection

    time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \
	hg38 calJac4) > rbest.log 2>&1 &
    # real    434m29.112s

    cat fb.hg38.chainRBest.CalJac4.txt
    # 2146650109 bases of 3110768607 (69.007%) in intersection

    # and for the swap:
    mkdir /hive/data/genomes/calJac4/bed/blastz.hg38.swap
    cd /hive/data/genomes/calJac4/bed/blastz.hg38.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/hg38/bed/lastzCalJac4.2020-08-03/DEF \
        -swap -chainMinScore=3000 -chainLinearGap=medium \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    #  real    105m30.938s

    cat fb.calJac4.chainHg38Link.txt
    # 2256668215 bases of 2859817025 (78.910%) in intersection
    cat fb.calJac4.chainSynHg38Link.txt
    # 2183912419 bases of 2859817025 (76.365%) in intersection

    time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \
	calJac4 hg38) > rbest.log 2>&1 &
    # real    467m22.590s

    cat fb.calJac4.chainRBest.Hg38.txt
    # 2147250913 bases of 2859817025 (75.084%) in intersection

############################################################################
# LASTZ MOUSE Rn7 (DONE - 2021-02-04 - Hiram)
    # can no longer use the lineage specific repeats with the new lastz
    # use a screen to manage this longish job:
    screen -S hg38Rn7

    mkdir /hive/data/genomes/hg38/bed/lastzRn7.2021-02-04
    cd /hive/data/genomes/hg38/bed/lastzRn7.2021-02-04

    # best to always specify an exact path to lastz so we know which one is used
    # lastz default parameters are human-mouse parameters

    printf '# human vs mouse
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz

# TARGET: Human Hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CTGDIR=/hive/data/genomes/hg38/hg38.contigs.2bit
SEQ1_CTGLEN=/hive/data/genomes/hg38/hg38.contigs.chrom.sizes
SEQ1_LIFT=/hive/data/genomes/hg38/jkStuff/hg38.contigs.lift
SEQ1_CHUNK=40000000
SEQ1_LAP=10000

# QUERY: Mouse Rn7
SEQ2_DIR=/hive/data/genomes/rn7/rn7.2bit
SEQ2_LEN=/hive/data/genomes/rn7/chrom.sizes
SEQ2_CHUNK=20000000
SEQ2_LAP=0

BASE=/hive/data/genomes/hg38/bed/lastzRn7.2021-02-04
TMPDIR=/dev/shm
' > DEF

    # verify files exist:
    grep "=" DEF | cut -d= -f2 | xargs ls -ogd

    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
        -chainMinScore=3000 -chainLinearGap=medium \
          -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
            -syntenicNet) > do.log 2>&1
    # real    270m41.393s

    sed -e 's/^/    # /;' fb.hg38.chainRn7Link.txt
    # 958592205 bases of 3110768607 (30.815%) in intersection
    sed -e 's/^/    # /;' fb.hg38.chainSynRn7Link.txt
    # 904066852 bases of 3110768607 (29.062%) in intersection

    time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \
	hg38 rn7) > rbest.log 2>&1 &
    # real    313m26.149s

    sed -e 's/^/    # /;' fb.hg38.chainRBest.Rn7.txt
    # 883775977 bases of 3110768607 (28.410%) in intersection

    #	and the swap
    mkdir /hive/data/genomes/rn7/bed/blastz.hg38.swap
    cd /hive/data/genomes/rn7/bed/blastz.hg38.swap
    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/hg38/bed/lastzRn7.2021-02-04/DEF \
        -chainMinScore=3000 -chainLinearGap=medium \
          -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
            -swap -syntenicNet) > swap.log 2>&1
    #   real    74m20.215s

    sed -e 's/^/    # /;' fb.rn7.chainHg38Link.txt
    # 928866703 bases of 2626580772 (35.364%) in intersection

    sed -e 's/^/    # /;' fb.rn7.chainSynHg38Link.txt
    # 879484562 bases of 2626580772 (33.484%) in intersection

    time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \
	rn7 hg38) > rbest.log 2>&1 &
    # real    373m6.610s

    sed -e 's/^/    # /;' fb.rn7.chainRBest.Hg38.txt
    # 885516265 bases of 2626580772 (33.714%) in intersection

#############################################################################
# LASTZ human/hg38 vs. X. tropicalis/xenTro10 - (DONE - 2021-02-22 - Hiram)
    mkdir /hive/data/genomes/hg38/bed/lastzXenTro10.2021-02-22
    cd /hive/data/genomes/hg38/bed/lastzXenTro10.2021-02-22

    printf '# human vs X. tropicalis
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz
BLASTZ_O=400
BLASTZ_E=30
BLASTZ_Y=3400
BLASTZ_L=6000
BLASTZ_K=2200
BLASTZ_M=50
BLASTZ_Q=/hive/data/staging/data/blastz/HoxD55.q
#      A    C    G    T
#     91  -90  -25 -100
#    -90  100 -100  -25
#    -25 -100  100  -90
#   -100  -25  -90  91

# TARGET: human hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CTGDIR=/hive/data/genomes/hg38/hg38.contigs.2bit
SEQ1_CTGLEN=/hive/data/genomes/hg38/hg38.contigs.chrom.sizes
SEQ1_LIFT=/hive/data/genomes/hg38/jkStuff/hg38.contigs.lift
SEQ1_CHUNK=40000000
SEQ1_LIMIT=10
SEQ1_LAP=10000

# QUERY: X. tropicalis xenTro10
SEQ2_DIR=/hive/data/genomes/xenTro10/xenTro10.2bit
SEQ2_LEN=/hive/data/genomes/xenTro10/chrom.sizes
SEQ2_CHUNK=20000000
SEQ2_LIMIT=20
SEQ2_LAP=0

BASE=/hive/data/genomes/hg38/bed/lastzXenTro10.2021-02-22
TMPDIR=/dev/shm
' > DEF

    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
        -chainMinScore=5000 -chainLinearGap=loose \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > do.log 2>&1 &
    # real    805m18.879s

    sed -e 's/^/    # /;' fb.hg38.chainXenTro10Link.txt
    # 146412457 bases of 3110768607 (4.707%) in intersection
    sed -e 's/^/    # /;' fb.hg38.chainSynXenTro10Link.txt
    # 41291684 bases of 3110768607 (1.327%) in intersection

 time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` hg38 xenTro10) \
       > rbest.log 2>&1 &
    # real    435m37.210s

    sed -e 's/^/    # /;' fb.hg38.chainRBest.XenTro10.txt
    # 73679844 bases of 3110768607 (2.369%) in intersection

    # and for the swap:
    mkdir /hive/data/genomes/xenTro10/bed/blastz.hg38.swap
    cd /hive/data/genomes/xenTro10/bed/blastz.hg38.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/hg38/bed/lastzXenTro10.2021-02-22/DEF \
        -swap -chainMinScore=5000 -chainLinearGap=loose \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    #  real    79m35.244s

    sed -e 's/^/    # /;' fb.xenTro10.chainHg38Link.txt
    # 150875559 bases of 1448461978 (10.416%) in intersection

    sed -e 's/^/    # /;' fb.xenTro10.chainSynHg38Link.txt
    # 40317510 bases of 1448461978 (2.783%) in intersection

  time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` xenTro10 hg38) \
       > rbest.log 2>&1
    # real    344m19.222s

    sed -e 's/^/    # /;' fb.xenTro10.chainRBest.Hg38.txt
    # 71467857 bases of 1448461978 (4.934%) in intersection

##############################################################################
# LASTZ Rambouillet sheep GCF_002742125.1 (DONE - 2021-04-05 - Hiram)
    mkdir /hive/data/genomes/hg38/bed/lastzGCF_002742125.1.2021-04-05
    cd /hive/data/genomes/hg38/bed/lastzGCF_002742125.1.2021-04-05

    printf '# GCF_002742125.1 vs hg38
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz
BLASTZ_T=2
BLASTZ_O=400
BLASTZ_E=30
BLASTZ_M=254
# default BLASTZ_Q score matrix:
#       A     C     G     T
# A    91  -114   -31  -123
# C  -114   100  -125   -31
# G   -31  -125   100  -114
# T  -123   -31  -114    91

# TARGET: Human Hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000

# QUERY: sheep GCF_002742125.1
SEQ2_DIR=/hive/data/genomes/asmHubs/GCF/002/742/125/GCF_002742125.1/GCF_002742125.1.2bit
SEQ2_LEN=/hive/data/genomes/asmHubs/GCF/002/742/125/GCF_002742125.1/GCF_002742125.1.chrom.sizes.txt
SEQ2_CHUNK=20000000
SEQ2_LAP=0
SEQ2_LIMIT=100

BASE=/hive/data/genomes/hg38/bed/lastzGCF_002742125.1.2021-04-05
TMPDIR=/dev/shm
' > DEF

export targetDb="hg38"
export asmId="GCF_002742125.1"
export gcPath="GCF/002/742/125"
cd /hive/data/genomes/$targetDb/bed/lastz${asmId}.2021-04-05
time (doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF \
   -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
     -syntenicNet -chainMinScore=3000 -chainLinearGap=medium) > do.log 2>&1
cat fb.${targetDb}.chain.${asmId}Link.txt
cat fb.${targetDb}.chainSyn.${asmId}Link.txt

grep -w real do.log | sed -e 's/^/    # /;'
    # real    180m56.099s


sed -e 's/^/    # /;' fb.$targetDb.chain.${asmId}Link.txt
    # 1410867422 bases of 3272116950 (43.118%) in intersection
sed -e 's/^/    # /;' fb.$targetDb.chainSyn.${asmId}Link.txt
    # 1349986710 bases of 3272116950 (41.257%) in intersection

time (doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
-query2Bit="/hive/data/genomes/asmHubs/$gcPath/${asmId}/${asmId}.2bit" \
-querySizes="/hive/data/genomes/asmHubs/$gcPath/${asmId}/${asmId}.chrom.sizes.txt" \
$targetDb ${asmId}) >> rbest.log 2>&1
grep -w real rbest.log | sed -e 's/^/    # /;'
    # real    353m30.968s

sed -e 's/^/    # /;' fb.$targetDb.chainRBest.$asmId.txt
    # 1279504252 bases of 3272116950 (39.103%) in intersection

### the swap to the assembly hub
export target="hg38"
export Target="Hg38"
export query="GCF_002742125.1"
export asmId="GCF_002742125.1_Oar_rambouillet_v1.0"
export gcPath="GCF/002/742/125"

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

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

sed -e 's/^/    # /;' fb.${query}.chain.${Target}Link.txt
    # 1399154667 bases of 2869914396 (48.752%) in intersection
sed -e 's/^/    # /;' fb.${query}.chainSyn.${Target}Link.txt
    # 1341190663 bases of 2869914396 (46.733%) in intersection

time (doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
-target2Bit="/hive/data/genomes/asmHubs/$gcPath/${query}/${query}.2bit" \
-targetSizes="/hive/data/genomes/asmHubs/$gcPath/${query}/${query}.chrom.sizes.txt" \
$query $target) >> rbest.log 2>&1
grep -w real rbest.log | sed -e 's/^/    # /;'
    # real    463m23.874s

sed -e 's/^/    # /;' fb.${query}.chainRBest.${Target}.txt
    # 1281096559 bases of 2869914396 (44.639%) in intersection

# Complete run time for all the swap operation:
    # real    554m2.489s

##############################################################################
# LASTZ human/hg38 vs. boxer/Tasha/canFam6
#	(DONE - 2021-05-17 - Hiram)

    mkdir /hive/data/genomes/hg38/bed/lastzCanFam6.2021-05-17
    cd /hive/data/genomes/hg38/bed/lastzCanFam6.2021-05-17

    printf '# human vs. dog (boxer Tasha)
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz
BLASTZ_M=254

# TARGET: human hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CTGDIR=/hive/data/genomes/hg38/hg38.contigs.2bit
SEQ1_CTGLEN=/hive/data/genomes/hg38/hg38.contigs.chrom.sizes
SEQ1_LIFT=/hive/data/genomes/hg38/jkStuff/hg38.contigs.lift
SEQ1_CHUNK=40000000
SEQ1_LIMIT=20
SEQ1_LAP=10000

# QUERY: boxer Tasha/canFam6
SEQ2_DIR=/hive/data/genomes/canFam6/canFam6.2bit
SEQ2_LEN=/hive/data/genomes/canFam6/chrom.sizes
SEQ2_CHUNK=20000000
SEQ2_LIMIT=20
SEQ2_LAP=0

BASE=/hive/data/genomes/hg38/bed/lastzCanFam6.2021-05-17
TMPDIR=/dev/shm
' > DEF

    time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl `pwd`/DEF \
        -verbose=2 -chainMinScore=3000 -chainLinearGap=medium \
          -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
            -syntenicNet) > do.log 2>&1
    # real    589m47.086s

    sed -e 's/^/    # /;' fb.hg38.chainCanFam6Link.txt
    # 1529157815 bases of 3110768607 (49.157%) in intersection

    sed -e 's/^/    # /;' fb.hg38.chainSynCanFam6Link.txt
    # 1468477892 bases of 3110768607 (47.206%) in intersection

    time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \
	hg38 canFam6) > rbest.log 2>&1 &
    # real    389m44.734s

    sed -e 's/^/    # /;' fb.hg38.chainRBest.CanFam6.txt
    # 1406453581 bases of 3110768607 (45.212%) in intersection

    # and for the swap:
    mkdir /hive/data/genomes/canFam6/bed/blastz.hg38.swap
    cd /hive/data/genomes/canFam6/bed/blastz.hg38.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/hg38/bed/lastzCanFam6.2021-05-17/DEF \
        -swap -chainMinScore=3000 -chainLinearGap=medium \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    #  real    84m5.076s

    sed -e 's/^/    # /;' fb.canFam6.chainHg38Link.txt
    # 1435515352 bases of 2312743346 (62.070%) in intersection
    sed -e 's/^/    # /;' fb.canFam6.chainSynHg38Link.txt
    # 1400962536 bases of 2312743346 (60.576%) in intersection

    time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \
	canFam6 hg38) > rbest.log 2>&1 &
    # real    270m7.152s

    sed -e 's/^/    # /;' fb.canFam6.chainRBest.Hg38.txt
    # 1406634909 bases of 2312743346 (60.821%) in intersection

############################################################################
# LASTZ Human Hg38 vs. goat GCF_001704415.1 (DONE - 2021-11-23 -Gerardo)

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

  time (~/kent/src/hg/utils/automation/pairLastz.sh \
	hg38 GCF_001704415.1_ARS1 primate mammal) \
	   > goatLiftOver_20211123.log 2>&1 &
  # check the total time
grep -w real  goatLiftOver_20211123.log  | tail -1 | sed -e 's/^/    # /;'
    # real      1388m21.601s

  # this  goatLiftOver_20211123.log log file happens to have a copy of the make doc, as well
  # as the copy of the make doc left in the target assembly directory:
# /hive/data/genomes/hg38/bed/lastzGCF_001704415.1.2021-11-23/makeDoc.txt

    # this command outputs this makeDoc text:

    cat kent/src/hg/utils/automation/goatLiftOver_20211123.log

##############################################################################
# LASTZ Human Hg38 vs. goat GCF_001704415.1
#    (DONE - 2021-11-23 - gperez2)

    mkdir /hive/data/genomes/hg38/bed/lastzGCF_001704415.1.2021-11-23
    cd /hive/data/genomes/hg38/bed/lastzGCF_001704415.1.2021-11-23

    printf '# goat GCF_001704415.1 vs. Human Hg38
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz

# TARGET: Human Hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
SEQ1_LIMIT=40

# QUERY: goat GCF_001704415.1
SEQ2_DIR=/hive/data/genomes/asmHubs/GCF/001/704/415/GCF_001704415.1/GCF_001704415.1.2bit
SEQ2_LEN=/hive/data/genomes/asmHubs/GCF/001/704/415/GCF_001704415.1/GCF_001704415.1.chrom.sizes.txt
SEQ2_CHUNK=20000000
SEQ2_LAP=0
SEQ2_LIMIT=100

BASE=/hive/data/genomes/hg38/bed/lastzGCF_001704415.1.2021-11-23
TMPDIR=/dev/shm

' > DEF

    time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \
       -qAsmId GCF_001704415.1_ARS1 -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
        -chainMinScore=3000 -chainLinearGap=medium) > do.log 2>&1
    grep -w real do.log | sed -e 's/^/    # /;'
    # real	495m30.622s

    sed -e 's/^/    # /;' fb.hg38.chainGCF_001704415.1Link.txt
    # 1420394090 bases of 3272116950 (43.409%) in intersection
    sed -e 's/^/    # /;' fb.hg38.chainSynGCF_001704415.1Link.txt
    # 1352717744 bases of 3272116950 (41.341%) in intersection

    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
       \
      -query2Bit="/hive/data/genomes/asmHubs/GCF/001/704/415/GCF_001704415.1/GCF_001704415.1.2bit" \
-querySizes="/hive/data/genomes/asmHubs/GCF/001/704/415/GCF_001704415.1/GCF_001704415.1.chrom.sizes.txt" \
        hg38 GCF_001704415.1) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	356m16.349s

    sed -e 's/^/    # /;' fb.hg38.chainRBest.GCF_001704415.1.txt
    # 1281979225 bases of 3272116950 (39.179%) in intersection

    ### and for the swap

    cd /hive/data/genomes/asmHubs/allBuild/GCF/001/704/415/GCF_001704415.1_ARS1/trackData/blastz.hg38.swap

   time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \
   -qAsmId GCF_001704415.1_ARS1 /hive/data/genomes/hg38/bed/lastzGCF_001704415.1.2021-11-23/DEF -swapDir=`pwd` \
  -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
    -chainMinScore=3000 -chainLinearGap=medium) > swap.log 2>&1

    grep -w real swap.log | sed -e 's/^/    # /;'
    # real	169m20.469s

    sed -e 's/^/    # /;' fb.GCF_001704415.1.chainHg38Link.txt
    # 1344964056 bases of 2922813246 (46.016%) in intersection
    sed -e 's/^/    # /;' fb.GCF_001704415.1.chainSynHg38Link.txt
    # 1290249255 bases of 2922813246 (44.144%) in intersection
\    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
    \
   -target2bit="/hive/data/genomes/asmHubs/GCF/001/704/415/GCF_001704415.1/GCF_001704415.1.2bit" \
-targetSizes="/hive/data/genomes/asmHubs/GCF/001/704/415/GCF_001704415.1/GCF_001704415.1.chrom.sizes.txt" \
   GCF_001704415.1 hg38) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	367m13.529s

    sed -e 's/^/    # /;' fb.GCF_001704415.1.chainRBest.Hg38.txt
    # 1283079843 bases of 2922813246 (43.899%) in intersection

##############################################################################
# LASTZ Human Hg38 vs. human GCA_009914755.4
#    (DONE - 2022-03-28 - hiram)

    mkdir /hive/data/genomes/hg38/bed/lastzGCA_009914755.4.2022-03-28
    cd /hive/data/genomes/hg38/bed/lastzGCA_009914755.4.2022-03-28

    printf '# human GCA_009914755.4 vs. Human Hg38
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz
BLASTZ_T=2
BLASTZ_O=600
BLASTZ_E=150
BLASTZ_M=254
BLASTZ_K=4500
BLASTZ_Y=15000
BLASTZ_Q=/hive/data/staging/data/blastz/human_chimp.v2.q
#       A     C     G     T
# A    90  -330  -236  -356
# C  -330   100  -318  -236
# G  -236  -318   100  -330
# T  -356  -236  -330    90

# TARGET: Human Hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
SEQ1_LIMIT=40

# QUERY: human GCA_009914755.4
SEQ2_DIR=/hive/data/genomes/asmHubs/GCA/009/914/755/GCA_009914755.4/GCA_009914755.4.2bit
SEQ2_LEN=/hive/data/genomes/asmHubs/GCA/009/914/755/GCA_009914755.4/GCA_009914755.4.chrom.sizes.txt
SEQ2_CHUNK=20000000
SEQ2_LAP=0
SEQ2_LIMIT=100

BASE=/hive/data/genomes/hg38/bed/lastzGCA_009914755.4.2022-03-28
TMPDIR=/dev/shm

' > DEF

    time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \
       -qAsmId GCA_009914755.4_CHM13_T2T_v2.0 -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
        -chainMinScore=5000 -chainLinearGap=medium) > do.log 2>&1
    grep -w real do.log | sed -e 's/^/    # /;'
    # real	357m59.184s

    sed -e 's/^/    # /;' fb.hg38.chainGCA_009914755.4Link.txt
    # 3037208207 bases of 3272116950 (92.821%) in intersection
    sed -e 's/^/    # /;' fb.hg38.chainSynGCA_009914755.4Link.txt
    # 3034364357 bases of 3272116950 (92.734%) in intersection

    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
       \
      -query2Bit="/hive/data/genomes/asmHubs/GCA/009/914/755/GCA_009914755.4/GCA_009914755.4.2bit" \
-querySizes="/hive/data/genomes/asmHubs/GCA/009/914/755/GCA_009914755.4/GCA_009914755.4.chrom.sizes.txt" \
        hg38 GCA_009914755.4) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	80m56.343s

    sed -e 's/^/    # /;' fb.hg38.chainRBest.GCA_009914755.4.txt
    # 2867463309 bases of 3272116950 (87.633%) in intersection

    ### and for the swap

    cd /hive/data/genomes/asmHubs/allBuild/GCA/009/914/755/GCA_009914755.4_CHM13_T2T_v2.0/trackData/blastz.hg38.swap

   time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \
   -qAsmId GCA_009914755.4_CHM13_T2T_v2.0 /hive/data/genomes/hg38/bed/lastzGCA_009914755.4.2022-03-28/DEF -swapDir=`pwd` \
  -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
    -chainMinScore=5000 -chainLinearGap=medium) > swap.log 2>&1

    grep -w real swap.log | sed -e 's/^/    # /;'
    # real	158m23.085s

    sed -e 's/^/    # /;' fb.GCA_009914755.4.chainHg38Link.txt
    # 2906145588 bases of 3117292070 (93.227%) in intersection
    sed -e 's/^/    # /;' fb.GCA_009914755.4.chainSynHg38Link.txt
    # 2896674405 bases of 3117292070 (92.923%) in intersection
\    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
    \
   -target2bit="/hive/data/genomes/asmHubs/GCA/009/914/755/GCA_009914755.4/GCA_009914755.4.2bit" \
-targetSizes="/hive/data/genomes/asmHubs/GCA/009/914/755/GCA_009914755.4/GCA_009914755.4.chrom.sizes.txt" \
   GCA_009914755.4 hg38) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	105m37.568s

    sed -e 's/^/    # /;' fb.GCA_009914755.4.chainRBest.Hg38.txt
    # 2863655887 bases of 3117292070 (91.864%) in intersection

##############################################################################
# LASTZ Human Hg38 vs. human GCA_021951015.1
#    (DONE - 2022-03-29 - hiram)

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

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

# TARGET: Human Hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
SEQ1_LIMIT=40

# QUERY: human GCA_021951015.1
SEQ2_DIR=/hive/data/genomes/asmHubs/GCA/021/951/015/GCA_021951015.1/GCA_021951015.1.2bit
SEQ2_LEN=/hive/data/genomes/asmHubs/GCA/021/951/015/GCA_021951015.1/GCA_021951015.1.chrom.sizes.txt
SEQ2_CHUNK=20000000
SEQ2_LAP=0
SEQ2_LIMIT=100

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

' > DEF

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

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

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

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

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

    ### and for the swap

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

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

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

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

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

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

##############################################################################
# LASTZ Human Hg38 vs. human GCA_021950905.1
#    (DONE - 2022-03-29 - hiram)

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

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

# TARGET: Human Hg38
SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
SEQ1_LIMIT=40

# QUERY: human GCA_021950905.1
SEQ2_DIR=/hive/data/genomes/asmHubs/GCA/021/950/905/GCA_021950905.1/GCA_021950905.1.2bit
SEQ2_LEN=/hive/data/genomes/asmHubs/GCA/021/950/905/GCA_021950905.1/GCA_021950905.1.chrom.sizes.txt
SEQ2_CHUNK=20000000
SEQ2_LAP=0
SEQ2_LIMIT=100

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

' > DEF

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

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

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

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

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

    ### and for the swap

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

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

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

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

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

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

##############################################################################
# LASTZ crab-eating macaque GCF_012559485.2 vs. Human Hg38
#    (DONE - 2022-05-25 - Jairo)

    mkdir /hive/data/genomes/asmHubs/allBuild/GCF/012/559/485/GCF_012559485.2_MFA1912RKSv2/trackData/lastzHg38.2022-05-25
    cd /hive/data/genomes/asmHubs/allBuild/GCF/012/559/485/GCF_012559485.2_MFA1912RKSv2/trackData/lastzHg38.2022-05-25

    printf '# Human Hg38 vs. crab-eating macaque GCF_012559485.2
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz
BLASTZ_T=2
BLASTZ_O=600
BLASTZ_E=150
BLASTZ_M=254
BLASTZ_K=4500
BLASTZ_Y=15000
BLASTZ_Q=/hive/data/staging/data/blastz/human_chimp.v2.q
#       A     C     G     T
# A    90  -330  -236  -356
# C  -330   100  -318  -236
# G  -236  -318   100  -330
# T  -356  -236  -330    90

# TARGET: crab-eating macaque 2021-10-26 GCF_012559485.2_MFA1912RKSv2
SEQ1_DIR=/hive/data/genomes/asmHubs/GCF/012/559/485/GCF_012559485.2/GCF_012559485.2.2bit
SEQ1_LEN=/hive/data/genomes/asmHubs/GCF/012/559/485/GCF_012559485.2/GCF_012559485.2.chrom.sizes.txt
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
SEQ1_LIMIT=40

# QUERY: Human  hg38
SEQ2_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ2_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ2_CHUNK=20000000
SEQ2_LAP=0
SEQ2_LIMIT=100

BASE=/hive/data/genomes/asmHubs/allBuild/GCF/012/559/485/GCF_012559485.2_MFA1912RKSv2/trackData/lastzHg38.2022-05-25
TMPDIR=/dev/shm

' > DEF

    time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \
      -tAsmId GCF_012559485.2_MFA1912RKSv2  -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
        -chainMinScore=5000 -chainLinearGap=medium) > do.log 2>&1
    grep -w real do.log | sed -e 's/^/    # /;'
    # real      1217m29.249s

    sed -e 's/^/    # /;' fb.GCF_012559485.2.chainHg38Link.txt
    # 2437888693 bases of 2800899072 (87.040%) in intersection
    sed -e 's/^/    # /;' fb.GCF_012559485.2.chainSynHg38Link.txt
    # 2421870400 bases of 2800899072 (86.468%) in intersection

    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
      -target2Bit="/hive/data/genomes/asmHubs/GCF/012/559/485/GCF_012559485.2/GCF_012559485.2.2bit" \
-targetSizes="/hive/data/genomes/asmHubs/GCF/012/559/485/GCF_012559485.2/GCF_012559485.2.chrom.sizes.txt" \
       \
        GCF_012559485.2 hg38) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real      144m18.277s

    sed -e 's/^/    # /;' fb.GCF_012559485.2.chainRBest.Hg38.txt
    # 2415126042 bases of 2800899072 (86.227%) in intersection

    ### and for the swap

    cd /hive/data/genomes/hg38/bed/blastz.GCF_012559485.2.swap

   time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \
  -tAsmId GCF_012559485.2_MFA1912RKSv2  /hive/data/genomes/asmHubs/allBuild/GCF/012/559/485/GCF_012559485.2_MFA1912RKSv2/trackData/lastzHg38.2022-05-25/DEF -swapDir=`pwd` \
  -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
    -chainMinScore=5000 -chainLinearGap=medium) > swap.log 2>&1

    grep -w real swap.log | sed -e 's/^/    # /;'
    # real      115m13.703s

    sed -e 's/^/    # /;' fb.hg38.chainGCF_012559485.2Link.txt
    # 2637306258 bases of 3272116950 (80.599%) in intersection
    sed -e 's/^/    # /;' fb.hg38.chainSynGCF_012559485.2Link.txt
    # 2602714449 bases of 3272116950 (79.542%) in intersection
\    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
   -query2bit="/hive/data/genomes/asmHubs/GCF/012/559/485/GCF_012559485.2/GCF_012559485.2.2bit" \
-querySizes="/hive/data/genomes/asmHubs/GCF/012/559/485/GCF_012559485.2/GCF_012559485.2.chrom.sizes.txt" \
    \
   hg38 GCF_012559485.2) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real      149m14.855s

    sed -e 's/^/    # /;' fb.hg38.chainRBest.GCF_012559485.2.txt
    # 2414467692 bases of 3272116950 (73.789%) in intersection

##############################################################################
# LASTZ Human Hg38 vs. crab-eating macaque GCA_011100615.1
#    (DONE - 2023-03-15 - Gerardo)

    mkdir /hive/data/genomes/hg38/bed/lastzGCA_011100615.1.2023-03-15
    cd /hive/data/genomes/hg38/bed/lastzGCA_011100615.1.2023-03-15

    printf '# crab-eating macaque GCA_011100615.1 vs. Human Hg38
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz
BLASTZ_T=2
BLASTZ_O=600
BLASTZ_E=150
BLASTZ_M=254
BLASTZ_K=4500
BLASTZ_Y=15000
BLASTZ_Q=/hive/data/staging/data/blastz/human_chimp.v2.q
#       A     C     G     T
# A    90  -330  -236  -356
# C  -330   100  -318  -236
# G  -236  -318   100  -330
# T  -356  -236  -330    90

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

# QUERY: crab-eating macaque 2020-03-10 GCA_011100615.1_Macaca_fascicularis_6.0
SEQ2_DIR=/hive/data/genomes/asmHubs/GCA/011/100/615/GCA_011100615.1/GCA_011100615.1.2bit
SEQ2_LEN=/hive/data/genomes/asmHubs/GCA/011/100/615/GCA_011100615.1/GCA_011100615.1.chrom.sizes.txt
SEQ2_CHUNK=20000000
SEQ2_LAP=0
SEQ2_LIMIT=100

BASE=/hive/data/genomes/hg38/bed/lastzGCA_011100615.1.2023-03-15
TMPDIR=/dev/shm

' > DEF

    time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \
       -qAsmId GCA_011100615.1_Macaca_fascicularis_6.0 -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
        -chainMinScore=5000 -chainLinearGap=medium) > do.log 2>&1
    grep -w real do.log | sed -e 's/^/    # /;'
    # real	130m22.412s

    sed -e 's/^/    # /;' fb.hg38.chainGCA_011100615.1Link.txt
    # 2631841536 bases of 3299210039 (79.772%) in intersection
    sed -e 's/^/    # /;' fb.hg38.chainSynGCA_011100615.1Link.txt
    # 2591533400 bases of 3299210039 (78.550%) in intersection

    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
       \
      -query2Bit="/hive/data/genomes/asmHubs/GCA/011/100/615/GCA_011100615.1/GCA_011100615.1.2bit" \
-querySizes="/hive/data/genomes/asmHubs/GCA/011/100/615/GCA_011100615.1/GCA_011100615.1.chrom.sizes.txt" \
        hg38 GCA_011100615.1) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	149m26.588s

    sed -e 's/^/    # /;' fb.hg38.chainRBest.GCA_011100615.1.txt
    # 2392058538 bases of 3299210039 (72.504%) in intersection

    ### and for the swap

    cd /hive/data/genomes/asmHubs/allBuild/GCA/011/100/615/GCA_011100615.1_Macaca_fascicularis_6.0/trackData/blastz.hg38.swap

   time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \
   -qAsmId GCA_011100615.1_Macaca_fascicularis_6.0 /hive/data/genomes/hg38/bed/lastzGCA_011100615.1.2023-03-15/DEF -swapDir=`pwd` \
  -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
    -chainMinScore=5000 -chainLinearGap=medium) > swap.log 2>&1

    grep -w real swap.log | sed -e 's/^/    # /;'
    # real	91m42.642s

    sed -e 's/^/    # /;' fb.GCA_011100615.1.chainHg38Link.txt
    # 2473727491 bases of 2906138557 (85.121%) in intersection
    sed -e 's/^/    # /;' fb.GCA_011100615.1.chainSynHg38Link.txt
    # 2446991743 bases of 2906138557 (84.201%) in intersection
\    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
    \
   -target2bit="/hive/data/genomes/asmHubs/GCA/011/100/615/GCA_011100615.1/GCA_011100615.1.2bit" \
-targetSizes="/hive/data/genomes/asmHubs/GCA/011/100/615/GCA_011100615.1/GCA_011100615.1.chrom.sizes.txt" \
   GCA_011100615.1 hg38) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	140m55.957s

    sed -e 's/^/    # /;' fb.GCA_011100615.1.chainRBest.Hg38.txt
    # 2394259873 bases of 2906138557 (82.386%) in intersection

real	512m28.587s
user	0m0.989s
sys	0m1.306s

##############################################################################
# LASTZ Human Hg38 vs. Human Hs1
#    (DONE - 2022-09-26 - hiram)

    mkdir /hive/data/genomes/hg38/bed/lastzHs1.2022-09-21
    cd /hive/data/genomes/hg38/bed/lastzHs1.2022-09-21

    printf '# Human Hs1 vs. Human Hg38
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz
BLASTZ_T=2
BLASTZ_O=600
BLASTZ_E=150
BLASTZ_M=254
BLASTZ_K=4500
BLASTZ_Y=15000
BLASTZ_Q=/hive/data/staging/data/blastz/human_chimp.v2.q
#       A     C     G     T
# A    90  -330  -236  -356
# C  -330   100  -318  -236
# G  -236  -318   100  -330
# T  -356  -236  -330    90

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

# QUERY: Human  hs1
SEQ2_DIR=/hive/data/genomes/hs1/hs1.2bit
SEQ2_LEN=/hive/data/genomes/hs1/chrom.sizes
SEQ2_CHUNK=20000000
SEQ2_LAP=0
SEQ2_LIMIT=100

BASE=/hive/data/genomes/hg38/bed/lastzHs1.2022-09-21
TMPDIR=/dev/shm

' > DEF

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

    sed -e 's/^/    # /;' fb.hg38.chainHs1Link.txt
    # 3037208207 bases of 3110768607 (97.635%) in intersection
    sed -e 's/^/    # /;' fb.hg38.chainSynHs1Link.txt
    # 3034364239 bases of 3110768607 (97.544%) in intersection

    time (~/kent/src/hg/utils/automation/doRecipBest.pl  -load -workhorse=hgwdev -buildDir=`pwd` \
       \
       \
        hg38 hs1) > rbest.log 2>&1

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

    sed -e 's/^/    # /;' fb.hg38.chainRBest.Hs1.txt

    ### and for the swap

    cd /hive/data/genomes/hs1/bed/blastz.hg38.swap

    time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -swap -verbose=2 \
       /hive/data/genomes/hg38/bed/lastzHs1.2022-09-21/DEF -swapDir=`pwd` \
-syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
        -chainMinScore=5000 -chainLinearGap=medium) > swap.log 2>&1

    grep -w real swap.log | sed -e 's/^/    # /;'
    # real      134m42.390s

    sed -e 's/^/    # /;' fb.hs1.chainHg38Link.txt
    # 2906145588 bases of 3117292070 (93.227%) in intersection
    sed -e 's/^/    # /;' fb.hs1.chainSynHg38Link.txt
    # 2896674405 bases of 3117292070 (92.923%) in intersection

    time (~/kent/src/hg/utils/automation/doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \
       hs1 hg38) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real      88m35.809s

    sed -e 's/^/    # /;' fb.hs1.chainRBest.Hg38.txt
    # 2863655887 bases of 3117292070 (91.864%) in intersection

##############################################################################
# LASTZ Human Hg38 vs. water buffalo GCF_019923935.1
#    (DONE - 2023-12-30 - mspeir)

    mkdir /hive/data/genomes/hg38/bed/lastzGCF_019923935.1.2023-12-30
    cd /hive/data/genomes/hg38/bed/lastzGCF_019923935.1.2023-12-30

    printf '# water buffalo GCF_019923935.1 vs. Human Hg38
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz

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

# QUERY: water buffalo 2021-09-10 GCF_019923935.1_NDDB_SH_1
SEQ2_DIR=/hive/data/genomes/asmHubs/GCF/019/923/935/GCF_019923935.1/GCF_019923935.1.2bit
SEQ2_LEN=/hive/data/genomes/asmHubs/GCF/019/923/935/GCF_019923935.1/GCF_019923935.1.chrom.sizes.txt
SEQ2_CHUNK=20000000
SEQ2_LAP=0
SEQ2_LIMIT=100

BASE=/hive/data/genomes/hg38/bed/lastzGCF_019923935.1.2023-12-30
TMPDIR=/dev/shm

' > DEF

    time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \
       -qAsmId GCF_019923935.1_NDDB_SH_1 -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
        -chainMinScore=3000 -chainLinearGap=medium) > do.log 2>&1
    grep -w real do.log | sed -e 's/^/    # /;'
    # real	931m33.045s

    sed -e 's/^/    # /;' fb.hg38.chainGCF_019923935.1Link.txt
    # 1441231401 bases of 3299210039 (43.684%) in intersection
    sed -e 's/^/    # /;' fb.hg38.chainSynGCF_019923935.1Link.txt
    # 1373195820 bases of 3299210039 (41.622%) in intersection

    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
       \
      -query2Bit="/hive/data/genomes/asmHubs/GCF/019/923/935/GCF_019923935.1/GCF_019923935.1.2bit" \
-querySizes="/hive/data/genomes/asmHubs/GCF/019/923/935/GCF_019923935.1/GCF_019923935.1.chrom.sizes.txt" \
        hg38 GCF_019923935.1) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	329m20.127s

    sed -e 's/^/    # /;' fb.hg38.chainRBest.GCF_019923935.1.txt
    # 1288371538 bases of 3299210039 (39.051%) in intersection

    ### and for the swap
# swap into: /hive/data/genomes/asmHubs/allBuild/GCF/019/923/935/GCF_019923935.1_NDDB_SH_1/trackData/blastz.hg38.swap
# running /hive/data/genomes/asmHubs/allBuild/GCF/019/923/935/GCF_019923935.1_NDDB_SH_1/trackData/blastz.hg38.swap/runSwap.sh
+ cd /hive/data/genomes/asmHubs/refseqBuild/GCF/019/923/935/GCF_019923935.1_NDDB_SH_1
+ export defaultName=GCF_019923935.1_NDDB_SH_1
+ defaultName=GCF_019923935.1_NDDB_SH_1
+ export asmId=GCF_019923935.1_NDDB_SH_1
+ asmId=GCF_019923935.1_NDDB_SH_1
+ export buildDir=/hive/data/genomes/asmHubs/refseqBuild/GCF/019/923/935/GCF_019923935.1_NDDB_SH_1
+ buildDir=/hive/data/genomes/asmHubs/refseqBuild/GCF/019/923/935/GCF_019923935.1_NDDB_SH_1
+ rm -f GCF_019923935.1_NDDB_SH_1.chromAlias.txt
+ ln -s trackData/chromAlias/GCF_019923935.1_NDDB_SH_1.chromAlias.txt .
+ '[' -s trackData/chromAlias/GCF_019923935.1_NDDB_SH_1.chromAlias.bb ']'
+ rm -f GCF_019923935.1_NDDB_SH_1.chromAlias.bb
+ ln -s trackData/chromAlias/GCF_019923935.1_NDDB_SH_1.chromAlias.bb .
+ /cluster/home/mspeir/kent/src/hg/utils/automation/asmHubTrackDb.sh GCF_019923935.1_NDDB_SH_1 GCF_019923935.1_NDDB_SH_1 /hive/data/genomes/asmHubs/refseqBuild/GCF/019/923/935/GCF_019923935.1_NDDB_SH_1
# no ensGene found
single chainNet
+ '[' 2 -ne 2 ']'
+ export asmId=GCF_019923935.1_NDDB_SH_1
+ asmId=GCF_019923935.1_NDDB_SH_1
+ export buildDir=/hive/data/genomes/asmHubs/refseqBuild/GCF/019/923/935/GCF_019923935.1_NDDB_SH_1
+ buildDir=/hive/data/genomes/asmHubs/refseqBuild/GCF/019/923/935/GCF_019923935.1_NDDB_SH_1
+ export hubLinks=/hive/data/genomes/asmHubs/hubLinks
+ hubLinks=/hive/data/genomes/asmHubs/hubLinks
+ export accessionId=GCF_019923935.1_NDDB_SH_1
+ accessionId=GCF_019923935.1_NDDB_SH_1
+ case ${asmId} in
++ echo GCF_019923935.1_NDDB_SH_1
++ awk -F_ '{printf "%s_%s", $1, $2}'
+ accessionId=GCF_019923935.1
+ export scriptDir=/cluster/home/mspeir/kent/src/hg/utils/automation
+ scriptDir=/cluster/home/mspeir/kent/src/hg/utils/automation
+ mkdir -p /hive/data/genomes/asmHubs/refseqBuild/GCF/019/923/935/GCF_019923935.1_NDDB_SH_1/bbi
+ mkdir -p /hive/data/genomes/asmHubs/refseqBuild/GCF/019/923/935/GCF_019923935.1_NDDB_SH_1/liftOver
+ export chainNetPriority=1
+ chainNetPriority=1
+ printf '# asmHubChainNetTrackDb.pl GCF_019923935.1_NDDB_SH_1 /hive/data/genomes/asmHubs/refseqBuild/GCF/019/923/935/GCF_019923935.1_NDDB_SH_1\n'
# asmHubChainNetTrackDb.pl GCF_019923935.1_NDDB_SH_1 /hive/data/genomes/asmHubs/refseqBuild/GCF/019/923/935/GCF_019923935.1_NDDB_SH_1
+ for D in '${buildDir}/trackData/lastz.*'
+ targetDb=GCF_019923935.1
++ basename /hive/data/genomes/asmHubs/refseqBuild/GCF/019/923/935/GCF_019923935.1_NDDB_SH_1/trackData/lastz.hg38
+ lastzDir=lastz.hg38
++ echo lastz.hg38
++ sed -e 's/lastz.//;'
+ otherDb=hg38
+ OtherDb=Hg38
++ ls -d /hive/data/genomes/asmHubs/refseqBuild/GCF/019/923/935/GCF_019923935.1_NDDB_SH_1/download/GCF_019923935.1_NDDB_SH_1_assembly_report.txt
+ asmReport=/hive/data/genomes/asmHubs/refseqBuild/GCF/019/923/935/GCF_019923935.1_NDDB_SH_1/download/GCF_019923935.1_NDDB_SH_1_assembly_report.txt
+ overChain=GCF_019923935.1.hg38.over.chain.gz
+ overToChain=GCF_019923935.1ToHg38.over.chain.gz
+ printf 'asmReport: %s\n' /hive/data/genomes/asmHubs/refseqBuild/GCF/019/923/935/GCF_019923935.1_NDDB_SH_1/download/GCF_019923935.1_NDDB_SH_1_assembly_report.txt
asmReport: /hive/data/genomes/asmHubs/refseqBuild/GCF/019/923/935/GCF_019923935.1_NDDB_SH_1/download/GCF_019923935.1_NDDB_SH_1_assembly_report.txt
+ '[' '!' -s /hive/data/genomes/asmHubs/refseqBuild/GCF/019/923/935/GCF_019923935.1_NDDB_SH_1/download/GCF_019923935.1_NDDB_SH_1_assembly_report.txt ']'
+ '[' '!' -s /hive/data/genomes/asmHubs/refseqBuild/GCF/019/923/935/GCF_019923935.1_NDDB_SH_1/trackData/lastz.hg38/axtChain/chainHg38.bb ']'
+ rm -f /hive/data/genomes/asmHubs/refseqBuild/GCF/019/923/935/GCF_019923935.1_NDDB_SH_1/bbi/GCF_019923935.1_NDDB_SH_1.chainHg38.bb
+ rm -f /hive/data/genomes/asmHubs/refseqBuild/GCF/019/923/935/GCF_019923935.1_NDDB_SH_1/bbi/GCF_019923935.1_NDDB_SH_1.chainHg38Link.bb
+ rm -f /hive/data/genomes/asmHubs/refseqBuild/GCF/019/923/935/GCF_019923935.1_NDDB_SH_1/bbi/GCF_019923935.1_NDDB_SH_1.chainSynHg38.bb
+ rm -f /hive/data/genomes/asmHubs/refseqBuild/GCF/019/923/935/GCF_019923935.1_NDDB_SH_1/bbi/GCF_019923935.1_NDDB_SH_1.chainSynHg38Link.bb
+ rm -f /hive/data/genomes/asmHubs/refseqBuild/GCF/019/923/935/GCF_019923935.1_NDDB_SH_1/bbi/GCF_019923935.1_NDDB_SH_1.chainRBestHg38.bb
+ rm -f /hive/data/genomes/asmHubs/refseqBuild/GCF/019/923/935/GCF_019923935.1_NDDB_SH_1/bbi/GCF_019923935.1_NDDB_SH_1.chainRBestHg38Link.bb
+ rm -f /hive/data/genomes/asmHubs/refseqBuild/GCF/019/923/935/GCF_019923935.1_NDDB_SH_1/bbi/GCF_019923935.1_NDDB_SH_1.chainLiftOverHg38.bb
+ rm -f /hive/data/genomes/asmHubs/refseqBuild/GCF/019/923/935/GCF_019923935.1_NDDB_SH_1/bbi/GCF_019923935.1_NDDB_SH_1.chainLiftOverHg38Link.bb
+ rm -f /hive/data/genomes/asmHubs/refseqBuild/GCF/019/923/935/GCF_019923935.1_NDDB_SH_1/bbi/GCF_019923935.1_NDDB_SH_1.hg38.net.bb
+ rm -f /hive/data/genomes/asmHubs/refseqBuild/GCF/019/923/935/GCF_019923935.1_NDDB_SH_1/bbi/GCF_019923935.1_NDDB_SH_1.hg38.net.summary.bb
+ rm -f /hive/data/genomes/asmHubs/refseqBuild/GCF/019/923/935/GCF_019923935.1_NDDB_SH_1/bbi/GCF_019923935.1_NDDB_SH_1.hg38.synNet.bb
+ rm -f /hive/data/genomes/asmHubs/refseqBuild/GCF/019/923/935/GCF_019923935.1_NDDB_SH_1/bbi/GCF_019923935.1_NDDB_SH_1.hg38.synNet.summary.bb
+ rm -f /hive/data/genomes/asmHubs/refseqBuild/GCF/019/923/935/GCF_019923935.1_NDDB_SH_1/bbi/GCF_019923935.1_NDDB_SH_1.hg38.rbestNet.bb
+ rm -f /hive/data/genomes/asmHubs/refseqBuild/GCF/019/923/935/GCF_019923935.1_NDDB_SH_1/bbi/GCF_019923935.1_NDDB_SH_1.hg38.rbestNet.summary.bb
+ rm -f /hive/data/genomes/asmHubs/refseqBuild/GCF/019/923/935/GCF_019923935.1_NDDB_SH_1/bbi/GCF_019923935.1_NDDB_SH_1.hg38.liftOverNet.bb
+ rm -f /hive/data/genomes/asmHubs/refseqBuild/GCF/019/923/935/GCF_019923935.1_NDDB_SH_1/bbi/GCF_019923935.1_NDDB_SH_1.hg38.liftOverNet.summary.bb
+ rm -f /hive/data/genomes/asmHubs/refseqBuild/GCF/019/923/935/GCF_019923935.1_NDDB_SH_1/liftOver/GCF_019923935.1ToHg38.over.chain.gz
+ '[' -s /hive/data/genomes/asmHubs/refseqBuild/GCF/019/923/935/GCF_019923935.1_NDDB_SH_1/trackData/lastz.hg38/axtChain/GCF_019923935.1.hg38.over.chain.gz ']'
+ ln -s ../trackData/lastz.hg38/axtChain/GCF_019923935.1.hg38.over.chain.gz /hive/data/genomes/asmHubs/refseqBuild/GCF/019/923/935/GCF_019923935.1_NDDB_SH_1/liftOver/GCF_019923935.1ToHg38.over.chain.gz
+ '[' -s /hive/data/genomes/asmHubs/refseqBuild/GCF/019/923/935/GCF_019923935.1_NDDB_SH_1/trackData/lastz.hg38/axtChain/chainHg38.bb ']'
+ ln -s ../trackData/lastz.hg38/axtChain/chainHg38.bb /hive/data/genomes/asmHubs/refseqBuild/GCF/019/923/935/GCF_019923935.1_NDDB_SH_1/bbi/GCF_019923935.1_NDDB_SH_1.chainHg38.bb
+ ln -s ../trackData/lastz.hg38/axtChain/chainHg38Link.bb /hive/data/genomes/asmHubs/refseqBuild/GCF/019/923/935/GCF_019923935.1_NDDB_SH_1/bbi/GCF_019923935.1_NDDB_SH_1.chainHg38Link.bb
+ '[' -s /hive/data/genomes/asmHubs/refseqBuild/GCF/019/923/935/GCF_019923935.1_NDDB_SH_1/trackData/lastz.hg38/bigMaf/GCF_019923935.1.hg38.net.bb ']'
+ ln -s ../trackData/lastz.hg38/bigMaf/GCF_019923935.1.hg38.net.bb /hive/data/genomes/asmHubs/refseqBuild/GCF/019/923/935/GCF_019923935.1_NDDB_SH_1/bbi/GCF_019923935.1_NDDB_SH_1.hg38.net.bb
+ ln -s ../trackData/lastz.hg38/bigMaf/GCF_019923935.1.hg38.net.summary.bb /hive/data/genomes/asmHubs/refseqBuild/GCF/019/923/935/GCF_019923935.1_NDDB_SH_1/bbi/GCF_019923935.1_NDDB_SH_1.hg38.net.summary.bb
+ '[' -s /hive/data/genomes/asmHubs/refseqBuild/GCF/019/923/935/GCF_019923935.1_NDDB_SH_1/trackData/lastz.hg38/axtChain/chainSynHg38.bb ']'
+ ln -s ../trackData/lastz.hg38/axtChain/chainSynHg38.bb /hive/data/genomes/asmHubs/refseqBuild/GCF/019/923/935/GCF_019923935.1_NDDB_SH_1/bbi/GCF_019923935.1_NDDB_SH_1.chainSynHg38.bb
+ ln -s ../trackData/lastz.hg38/axtChain/chainSynHg38Link.bb /hive/data/genomes/asmHubs/refseqBuild/GCF/019/923/935/GCF_019923935.1_NDDB_SH_1/bbi/GCF_019923935.1_NDDB_SH_1.chainSynHg38Link.bb
+ '[' -s /hive/data/genomes/asmHubs/refseqBuild/GCF/019/923/935/GCF_019923935.1_NDDB_SH_1/trackData/lastz.hg38/bigMaf/GCF_019923935.1.hg38.synNet.bb ']'
+ ln -s ../trackData/lastz.hg38/bigMaf/GCF_019923935.1.hg38.synNet.bb /hive/data/genomes/asmHubs/refseqBuild/GCF/019/923/935/GCF_019923935.1_NDDB_SH_1/bbi/GCF_019923935.1_NDDB_SH_1.hg38.synNet.bb
+ ln -s ../trackData/lastz.hg38/bigMaf/GCF_019923935.1.hg38.synNet.summary.bb /hive/data/genomes/asmHubs/refseqBuild/GCF/019/923/935/GCF_019923935.1_NDDB_SH_1/bbi/GCF_019923935.1_NDDB_SH_1.hg38.synNet.summary.bb
+ '[' -s /hive/data/genomes/asmHubs/refseqBuild/GCF/019/923/935/GCF_019923935.1_NDDB_SH_1/trackData/lastz.hg38/axtChain/chainRBestHg38.bb ']'
+ ln -s ../trackData/lastz.hg38/axtChain/chainRBestHg38.bb /hive/data/genomes/asmHubs/refseqBuild/GCF/019/923/935/GCF_019923935.1_NDDB_SH_1/bbi/GCF_019923935.1_NDDB_SH_1.chainRBestHg38.bb
+ ln -s ../trackData/lastz.hg38/axtChain/chainRBestHg38Link.bb /hive/data/genomes/asmHubs/refseqBuild/GCF/019/923/935/GCF_019923935.1_NDDB_SH_1/bbi/GCF_019923935.1_NDDB_SH_1.chainRBestHg38Link.bb
+ '[' -s /hive/data/genomes/asmHubs/refseqBuild/GCF/019/923/935/GCF_019923935.1_NDDB_SH_1/trackData/lastz.hg38/bigMaf/GCF_019923935.1.hg38.rbestNet.bb ']'
+ ln -s ../trackData/lastz.hg38/bigMaf/GCF_019923935.1.hg38.rbestNet.bb /hive/data/genomes/asmHubs/refseqBuild/GCF/019/923/935/GCF_019923935.1_NDDB_SH_1/bbi/GCF_019923935.1_NDDB_SH_1.hg38.rbestNet.bb
+ ln -s ../trackData/lastz.hg38/bigMaf/GCF_019923935.1.hg38.rbestNet.summary.bb /hive/data/genomes/asmHubs/refseqBuild/GCF/019/923/935/GCF_019923935.1_NDDB_SH_1/bbi/GCF_019923935.1_NDDB_SH_1.hg38.rbestNet.summary.bb
+ '[' -s /hive/data/genomes/asmHubs/refseqBuild/GCF/019/923/935/GCF_019923935.1_NDDB_SH_1/trackData/lastz.hg38/axtChain/chainLiftOverHg38.bb ']'
+ printf '# there is NO chainLiftOverHg38.bb\n'
# there is NO chainLiftOverHg38.bb
++ cut -c1-2
++ echo hg38
+ otherPrefix=hg
+ '[' hg = GC ']'
++ hgsql -N -e 'select organism from dbDb where name="hg38"' hgcentraltest
+ organism=Human
++ hgsql -N -e 'select scientificName from dbDb where name="hg38"' hgcentraltest
+ sciName='Homo sapiens'
++ hgsql -N -e 'select taxId from dbDb where name="hg38"' hgcentraltest
+ taxId=9606
++ hgsql -N -e 'select description from dbDb where name="hg38"' hgcentraltest
+ o_date='Dec. 2013 (GRCh38/hg38)'
++ /cluster/home/mspeir/kent/src/hg/utils/phyloTrees/findScores.pl hg38 GCF_019923935.1
++ grep matrix
+ matrix='matrix 16 91,-114,-31,-123,-114,100,-125,-31,-31,-125,100,-114,-123,-31,-114,91'
++ echo hg38
++ cut -c1-2
+ otherPrefix=hg
+ '[' hg = GC ']'
++ hgsql -N -e 'select organism from dbDb where name="hg38"' hgcentraltest
+ organism=Human
++ hgsql -N -e 'select scientificName from dbDb where name="hg38"' hgcentraltest
+ sciName='Homo sapiens'
++ hgsql -N -e 'select taxId from dbDb where name="hg38"' hgcentraltest
+ taxId=9606
++ hgsql -N -e 'select description from dbDb where name="hg38"' hgcentraltest
+ o_date='Dec. 2013 (GRCh38/hg38)'
++ /cluster/home/mspeir/kent/src/hg/utils/phyloTrees/findScores.pl hg38 GCF_019923935.1
++ grep matrix
+ matrix='matrix 16 91,-114,-31,-123,-114,100,-125,-31,-31,-125,100,-114,-123,-31,-114,91'
++ /cluster/home/mspeir/kent/src/hg/utils/phyloTrees/findScores.pl hg38 GCF_019923935.1
++ grep MinScore
+ minScore='chainMinScore 3000'
++ /cluster/home/mspeir/kent/src/hg/utils/phyloTrees/findScores.pl hg38 GCF_019923935.1
++ grep LinearGap
+ linGap='chainLinearGap medium'
+ printf '##############################################################################
# hg38 - Human - Homo sapiens - taxId: 9606
##############################################################################
'
+ printf 'track chainNetHg38
compositeTrack on
shortLabel Human Chain/Net
longLabel Human (Dec. 2013 (GRCh38/hg38)), Chain and Net Alignments
subGroup1 view Views chain=Chain net=Net
dragAndDrop subTracks
visibility hide
group compGeno
'
+ printf 'priority 100.1
color 0,0,0
altColor 100,50,0
type bed 3
sortOrder view=+
'
+ '[' 'xmatrix 16 91,-114,-31,-123,-114,100,-125,-31,-31,-125,100,-114,-123,-31,-114,91y' = xy ']'
+ printf 'matrix 16 91,-114,-31,-123,-114,100,-125,-31,-31,-125,100,-114,-123,-31,-114,91
chainMinScore 3000
chainLinearGap medium
matrixHeader A, C, G, T
otherDb hg38
html html/GCF_019923935.1_NDDB_SH_1.chainNet

'
+ printf '    track chainNetHg38Viewchain
    shortLabel Chain
    view chain
    visibility pack
    parent chainNetHg38
    spectrum on

        track chainHg38
        parent chainNetHg38Viewchain
        subGroups view=chain
        shortLabel Human Chain
        longLabel Human (Dec. 2013 (GRCh38/hg38)) Chained Alignments
        type bigChain hg38
        bigDataUrl bbi/GCF_019923935.1_NDDB_SH_1.chainHg38.bb
        linkDataUrl bbi/GCF_019923935.1_NDDB_SH_1.chainHg38Link.bb
        priority %d

' 1
+ '[' -s /hive/data/genomes/asmHubs/refseqBuild/GCF/019/923/935/GCF_019923935.1_NDDB_SH_1/bbi/GCF_019923935.1_NDDB_SH_1.chainSynHg38.bb ']'
+ printf '        track chainSynHg38
        parent chainNetHg38Viewchain
        subGroups view=chain
        shortLabel Human synChain
        longLabel Human (Dec. 2013 (GRCh38/hg38)) Syntenic Chained Alignments
        type bigChain hg38
        bigDataUrl bbi/GCF_019923935.1_NDDB_SH_1.chainSynHg38.bb
        linkDataUrl bbi/GCF_019923935.1_NDDB_SH_1.chainSynHg38Link.bb
        priority %d

' 2
+ '[' -s /hive/data/genomes/asmHubs/refseqBuild/GCF/019/923/935/GCF_019923935.1_NDDB_SH_1/bbi/GCF_019923935.1_NDDB_SH_1.chainRBestHg38.bb ']'
+ printf '        track chainRBestHg38
        parent chainNetHg38Viewchain
        subGroups view=chain
        shortLabel Human rbChain
        longLabel Human (Dec. 2013 (GRCh38/hg38)) Reciprocal Best Chained Alignments
        type bigChain hg38
        bigDataUrl bbi/GCF_019923935.1_NDDB_SH_1.chainRBestHg38.bb
        linkDataUrl bbi/GCF_019923935.1_NDDB_SH_1.chainRBestHg38Link.bb
        priority %d

' 3
+ '[' -s /hive/data/genomes/asmHubs/refseqBuild/GCF/019/923/935/GCF_019923935.1_NDDB_SH_1/bbi/GCF_019923935.1_NDDB_SH_1.chainLiftOverHg38.bb ']'
+ printf '    track mafNetHg38Viewnet
    shortLabel Net
    view net
    visibility full
    parent chainNetHg38

        track netHg38
        parent mafNetHg38Viewnet
        subGroups view=net
        shortLabel Human net
        longLabel Human (Dec. 2013 (GRCh38/hg38)) Net Alignment
        type bigMaf
        bigDataUrl bbi/GCF_019923935.1_NDDB_SH_1.hg38.net.bb
        summary bbi/GCF_019923935.1_NDDB_SH_1.hg38.net.summary.bb
        speciesOrder hg38
        priority %d

' 4
+ '[' -s /hive/data/genomes/asmHubs/refseqBuild/GCF/019/923/935/GCF_019923935.1_NDDB_SH_1/bbi/GCF_019923935.1_NDDB_SH_1.hg38.synNet.summary.bb ']'
+ printf '        track synNetHg38
        parent mafNetHg38Viewnet
        subGroups view=net
        shortLabel Human synNet
        longLabel Human (Dec. 2013 (GRCh38/hg38)) Syntenic Net Alignment
        type bigMaf
        bigDataUrl bbi/GCF_019923935.1_NDDB_SH_1.hg38.synNet.bb
        summary bbi/GCF_019923935.1_NDDB_SH_1.hg38.synNet.summary.bb
        speciesOrder hg38
        priority %d

' 5
+ '[' -s /hive/data/genomes/asmHubs/refseqBuild/GCF/019/923/935/GCF_019923935.1_NDDB_SH_1/bbi/GCF_019923935.1_NDDB_SH_1.hg38.rbestNet.summary.bb ']'
+ printf '        track rbestNetHg38
        parent mafNetHg38Viewnet
        subGroups view=net
        shortLabel Human rbestNet
        longLabel Human (Dec. 2013 (GRCh38/hg38)) Reciprocal Best Net Alignment
        type bigMaf
        bigDataUrl bbi/GCF_019923935.1_NDDB_SH_1.hg38.rbestNet.bb
        summary bbi/GCF_019923935.1_NDDB_SH_1.hg38.rbestNet.summary.bb
        speciesOrder hg38
        priority %d

' 6
+ '[' -s /hive/data/genomes/asmHubs/refseqBuild/GCF/019/923/935/GCF_019923935.1_NDDB_SH_1/bbi/GCF_019923935.1_NDDB_SH_1.hg38.liftOverNet.summary.bb ']'
##############################################################################
# LASTZ Human Hg38 vs. water buffalo GCF_019923935.1
#    (DONE - 2023-12-30 - mspeir)

    mkdir /hive/data/genomes/hg38/bed/lastzGCF_019923935.1.2023-12-30
    cd /hive/data/genomes/hg38/bed/lastzGCF_019923935.1.2023-12-30

    printf '# water buffalo GCF_019923935.1 vs. Human Hg38
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz

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

# QUERY: water buffalo 2021-09-10 GCF_019923935.1_NDDB_SH_1
SEQ2_DIR=/hive/data/genomes/asmHubs/GCF/019/923/935/GCF_019923935.1/GCF_019923935.1.2bit
SEQ2_LEN=/hive/data/genomes/asmHubs/GCF/019/923/935/GCF_019923935.1/GCF_019923935.1.chrom.sizes.txt
SEQ2_CHUNK=20000000
SEQ2_LAP=0
SEQ2_LIMIT=100

BASE=/hive/data/genomes/hg38/bed/lastzGCF_019923935.1.2023-12-30
TMPDIR=/dev/shm

' > DEF

    time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \
       -qAsmId GCF_019923935.1_NDDB_SH_1 -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
        -chainMinScore=3000 -chainLinearGap=medium) > do.log 2>&1
    grep -w real do.log | sed -e 's/^/    # /;'
    # real	931m33.045s

    sed -e 's/^/    # /;' fb.hg38.chainGCF_019923935.1Link.txt
    # 1441231401 bases of 3299210039 (43.684%) in intersection
    sed -e 's/^/    # /;' fb.hg38.chainSynGCF_019923935.1Link.txt
    # 1373195820 bases of 3299210039 (41.622%) in intersection

    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
       \
      -query2Bit="/hive/data/genomes/asmHubs/GCF/019/923/935/GCF_019923935.1/GCF_019923935.1.2bit" \
-querySizes="/hive/data/genomes/asmHubs/GCF/019/923/935/GCF_019923935.1/GCF_019923935.1.chrom.sizes.txt" \
        hg38 GCF_019923935.1) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	329m20.127s

    sed -e 's/^/    # /;' fb.hg38.chainRBest.GCF_019923935.1.txt
    # 1288371538 bases of 3299210039 (39.051%) in intersection

    ### and for the swap

    cd /hive/data/genomes/asmHubs/allBuild/GCF/019/923/935/GCF_019923935.1_NDDB_SH_1/trackData/blastz.hg38.swap

   time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \
   -qAsmId GCF_019923935.1_NDDB_SH_1 /hive/data/genomes/hg38/bed/lastzGCF_019923935.1.2023-12-30/DEF -swapDir=`pwd` \
  -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
    -chainMinScore=3000 -chainLinearGap=medium) > swap.log 2>&1

    grep -w real swap.log | sed -e 's/^/    # /;'
    # real	205m7.620s

    sed -e 's/^/    # /;' fb.GCF_019923935.1.chainHg38Link.txt
    # 1334547184 bases of 2622460639 (50.889%) in intersection
    sed -e 's/^/    # /;' fb.GCF_019923935.1.chainSynHg38Link.txt
    # 1298033146 bases of 2622460639 (49.497%) in intersection
\    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
    \
   -target2bit="/hive/data/genomes/asmHubs/GCF/019/923/935/GCF_019923935.1/GCF_019923935.1.2bit" \
-targetSizes="/hive/data/genomes/asmHubs/GCF/019/923/935/GCF_019923935.1/GCF_019923935.1.chrom.sizes.txt" \
   GCF_019923935.1 hg38) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	316m37.285s

    sed -e 's/^/    # /;' fb.GCF_019923935.1.chainRBest.Hg38.txt
    # 1289247133 bases of 2622460639 (49.162%) in intersection

real	1782m42.747s
user	0m2.954s
sys	0m2.951s

##############################################################################
# LASTZ Human Hg38 vs. rodents GCA_023856395.1
#    (DONE - 2024-03-30 - Gerardo)

    mkdir /hive/data/genomes/hg38/bed/lastzGCA_023856395.1.2024-03-30
    cd /hive/data/genomes/hg38/bed/lastzGCA_023856395.1.2024-03-30

    printf '# rodents GCA_023856395.1 vs. Human Hg38
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz

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

# QUERY: rodents 2022-06-29 GCA_023856395.1_Psun_UM_1.1
SEQ2_DIR=/hive/data/genomes/asmHubs/GCA/023/856/395/GCA_023856395.1/GCA_023856395.1.2bit
SEQ2_LEN=/hive/data/genomes/asmHubs/GCA/023/856/395/GCA_023856395.1/GCA_023856395.1.chrom.sizes.txt
SEQ2_CHUNK=20000000
SEQ2_LAP=0
SEQ2_LIMIT=100

BASE=/hive/data/genomes/hg38/bed/lastzGCA_023856395.1.2024-03-30
TMPDIR=/dev/shm

' > DEF

    time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \
       -qAsmId GCA_023856395.1_Psun_UM_1.1 -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
        -chainMinScore=3000 -chainLinearGap=medium) > do.log 2>&1
    grep -w real do.log | sed -e 's/^/    # /;'
    # real	354m48.970s

    sed -e 's/^/    # /;' fb.hg38.chainGCA_023856395.1Link.txt
    # 950913494 bases of 3299210039 (28.822%) in intersection
    sed -e 's/^/    # /;' fb.hg38.chainSynGCA_023856395.1Link.txt
    # 899516133 bases of 3299210039 (27.265%) in intersection

    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
       \
      -query2Bit="/hive/data/genomes/asmHubs/GCA/023/856/395/GCA_023856395.1/GCA_023856395.1.2bit" \
-querySizes="/hive/data/genomes/asmHubs/GCA/023/856/395/GCA_023856395.1/GCA_023856395.1.chrom.sizes.txt" \
        hg38 GCA_023856395.1) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	223m6.402s

    sed -e 's/^/    # /;' fb.hg38.chainRBest.GCA_023856395.1.txt
    # 856925550 bases of 3299210039 (25.974%) in intersection

    ### and for the swap

    cd /hive/data/genomes/asmHubs/allBuild/GCA/023/856/395/GCA_023856395.1_Psun_UM_1.1/trackData/blastz.hg38.swap

   time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \
   -qAsmId GCA_023856395.1_Psun_UM_1.1 /hive/data/genomes/hg38/bed/lastzGCA_023856395.1.2024-03-30/DEF -swapDir=`pwd` \
  -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
    -chainMinScore=3000 -chainLinearGap=medium) > swap.log 2>&1

    grep -w real swap.log | sed -e 's/^/    # /;'
    # real	52m5.776s

    sed -e 's/^/    # /;' fb.GCA_023856395.1.chainHg38Link.txt
    # 877678504 bases of 2119204330 (41.415%) in intersection
    sed -e 's/^/    # /;' fb.GCA_023856395.1.chainSynHg38Link.txt
    # 852484293 bases of 2119204330 (40.227%) in intersection
\    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
    \
   -target2bit="/hive/data/genomes/asmHubs/GCA/023/856/395/GCA_023856395.1/GCA_023856395.1.2bit" \
-targetSizes="/hive/data/genomes/asmHubs/GCA/023/856/395/GCA_023856395.1/GCA_023856395.1.chrom.sizes.txt" \
   GCA_023856395.1 hg38) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	224m13.370s

    sed -e 's/^/    # /;' fb.GCA_023856395.1.chainRBest.Hg38.txt
    # 858590864 bases of 2119204330 (40.515%) in intersection

real	854m18.020s
user	0m2.527s
sys	0m2.820s
##############################################################################
# LASTZ Human Hg38 vs. alpaca GCF_000164845.4
#    (DONE - 2024-05-06 - Gerardo)

    mkdir /hive/data/genomes/hg38/bed/lastzGCF_000164845.4.2024-05-06
    cd /hive/data/genomes/hg38/bed/lastzGCF_000164845.4.2024-05-06

    printf '# alpaca GCF_000164845.4 vs. Human Hg38
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz

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

# QUERY: alpaca 2019-07-15 GCF_000164845.4_VicPac3.2
SEQ2_DIR=/hive/data/genomes/asmHubs/GCF/000/164/845/GCF_000164845.4/GCF_000164845.4.2bit
SEQ2_LEN=/hive/data/genomes/asmHubs/GCF/000/164/845/GCF_000164845.4/GCF_000164845.4.chrom.sizes.txt
SEQ2_CHUNK=20000000
SEQ2_LAP=0
SEQ2_LIMIT=500

BASE=/hive/data/genomes/hg38/bed/lastzGCF_000164845.4.2024-05-06
TMPDIR=/dev/shm

' > DEF

    time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \
       -qAsmId GCF_000164845.4_VicPac3.2 -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
        -chainMinScore=3000 -chainLinearGap=medium) > do.log 2>&1
    grep -w real do.log | sed -e 's/^/    # /;'
    # real	571m35.449s

    sed -e 's/^/    # /;' fb.hg38.chainGCF_000164845.4Link.txt
    # 1529610386 bases of 3299210039 (46.363%) in intersection
    sed -e 's/^/    # /;' fb.hg38.chainSynGCF_000164845.4Link.txt
    # 1453627877 bases of 3299210039 (44.060%) in intersection

    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
       \
      -query2Bit="/hive/data/genomes/asmHubs/GCF/000/164/845/GCF_000164845.4/GCF_000164845.4.2bit" \
-querySizes="/hive/data/genomes/asmHubs/GCF/000/164/845/GCF_000164845.4/GCF_000164845.4.chrom.sizes.txt" \
        hg38 GCF_000164845.4) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	232m20.310s

    sed -e 's/^/    # /;' fb.hg38.chainRBest.GCF_000164845.4.txt
    # 1365760344 bases of 3299210039 (41.397%) in intersection

    ### and for the swap

    cd /hive/data/genomes/asmHubs/allBuild/GCF/000/164/845/GCF_000164845.4_VicPac3.2/trackData/blastz.hg38.swap

   time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \
   -qAsmId GCF_000164845.4_VicPac3.2 /hive/data/genomes/hg38/bed/lastzGCF_000164845.4.2024-05-06/DEF -swapDir=`pwd` \
  -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
    -chainMinScore=3000 -chainLinearGap=medium) > swap.log 2>&1

    grep -w real swap.log | sed -e 's/^/    # /;'
    # real	86m46.535s

    sed -e 's/^/    # /;' fb.GCF_000164845.4.chainHg38Link.txt
    # 1421872969 bases of 2118870233 (67.105%) in intersection
    sed -e 's/^/    # /;' fb.GCF_000164845.4.chainSynHg38Link.txt
    # 1369075156 bases of 2118870233 (64.613%) in intersection
\    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
    \
   -target2bit="/hive/data/genomes/asmHubs/GCF/000/164/845/GCF_000164845.4/GCF_000164845.4.2bit" \
-targetSizes="/hive/data/genomes/asmHubs/GCF/000/164/845/GCF_000164845.4/GCF_000164845.4.chrom.sizes.txt" \
   GCF_000164845.4 hg38) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	306m47.213s

    sed -e 's/^/    # /;' fb.GCF_000164845.4.chainRBest.Hg38.txt
    # 1366946875 bases of 2118870233 (64.513%) in intersection

real	1197m34.536s
user	0m3.691s
sys	0m4.207s
##############################################################################
# LASTZ American alligator GCF_030867095.1 vs. Human Hg38
#    (DONE - 2024-05-24 - Gerardo)

    mkdir /hive/data/genomes/asmHubs/allBuild/GCF/030/867/095/GCF_030867095.1_rAllMis1/trackData/lastzHg38.2024-05-24
    cd /hive/data/genomes/asmHubs/allBuild/GCF/030/867/095/GCF_030867095.1_rAllMis1/trackData/lastzHg38.2024-05-24

    printf '# Human Hg38 vs. American alligator GCF_030867095.1
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz

# TARGET: American alligator 2023-08-24 GCF_030867095.1_rAllMis1
SEQ1_DIR=/hive/data/genomes/asmHubs/GCF/030/867/095/GCF_030867095.1/GCF_030867095.1.2bit
SEQ1_LEN=/hive/data/genomes/asmHubs/GCF/030/867/095/GCF_030867095.1/GCF_030867095.1.chrom.sizes.txt
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
SEQ1_LIMIT=40

# QUERY: Human  hg38
SEQ2_DIR=/hive/data/genomes/hg38/hg38.2bit
SEQ2_LEN=/hive/data/genomes/hg38/chrom.sizes
SEQ2_CHUNK=20000000
SEQ2_LAP=0
SEQ2_LIMIT=100

BASE=/hive/data/genomes/asmHubs/allBuild/GCF/030/867/095/GCF_030867095.1_rAllMis1/trackData/lastzHg38.2024-05-24
TMPDIR=/dev/shm

' > DEF

    time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \
      -tAsmId GCF_030867095.1_rAllMis1  -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
        -chainMinScore=5000 -chainLinearGap=loose) > do.log 2>&1
    grep -w real do.log | sed -e 's/^/    # /;'
    # real	249m13.680s

    sed -e 's/^/    # /;' fb.GCF_030867095.1.chainHg38Link.txt
    # 100244204 bases of 2346795873 (4.272%) in intersection
    sed -e 's/^/    # /;' fb.GCF_030867095.1.chainSynHg38Link.txt
    # 82875962 bases of 2346795873 (3.531%) in intersection

    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
      -target2Bit="/hive/data/genomes/asmHubs/GCF/030/867/095/GCF_030867095.1/GCF_030867095.1.2bit" \
-targetSizes="/hive/data/genomes/asmHubs/GCF/030/867/095/GCF_030867095.1/GCF_030867095.1.chrom.sizes.txt" \
       \
        GCF_030867095.1 hg38) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	115m18.304s

    sed -e 's/^/    # /;' fb.GCF_030867095.1.chainRBest.Hg38.txt
    # 86384977 bases of 2346795873 (3.681%) in intersection

    ### and for the swap

    cd /hive/data/genomes/hg38/bed/blastz.GCF_030867095.1.swap

   time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \
  -tAsmId GCF_030867095.1_rAllMis1  /hive/data/genomes/asmHubs/allBuild/GCF/030/867/095/GCF_030867095.1_rAllMis1/trackData/lastzHg38.2024-05-24/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	9m9.709s

    sed -e 's/^/    # /;' fb.hg38.chainGCF_030867095.1Link.txt
    # 112908581 bases of 3299210039 (3.422%) in intersection
    sed -e 's/^/    # /;' fb.hg38.chainSynGCF_030867095.1Link.txt
    # 84530241 bases of 3299210039 (2.562%) in intersection
\    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
   -query2bit="/hive/data/genomes/asmHubs/GCF/030/867/095/GCF_030867095.1/GCF_030867095.1.2bit" \
-querySizes="/hive/data/genomes/asmHubs/GCF/030/867/095/GCF_030867095.1/GCF_030867095.1.chrom.sizes.txt" \
    \
   hg38 GCF_030867095.1) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	142m21.697s

    sed -e 's/^/    # /;' fb.hg38.chainRBest.GCF_030867095.1.txt
    # 86433905 bases of 3299210039 (2.620%) in intersection

real	516m8.051s
user	0m2.513s
sys	0m2.893s
##############################################################################
# LASTZ Human Hg38 vs. rabbit GCF_009806435.1
#    (DONE - 2024-06-28 - Gerardo)

    mkdir /hive/data/genomes/hg38/bed/lastzGCF_009806435.1.2024-06-28
    cd /hive/data/genomes/hg38/bed/lastzGCF_009806435.1.2024-06-28

    printf '# rabbit GCF_009806435.1 vs. Human Hg38
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz

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

# QUERY: rabbit 2021-02-04 GCF_009806435.1_UM_NZW_1.0
SEQ2_DIR=/hive/data/genomes/asmHubs/GCF/009/806/435/GCF_009806435.1/GCF_009806435.1.2bit
SEQ2_LEN=/hive/data/genomes/asmHubs/GCF/009/806/435/GCF_009806435.1/GCF_009806435.1.chrom.sizes.txt
SEQ2_CHUNK=20000000
SEQ2_LAP=0
SEQ2_LIMIT=100

BASE=/hive/data/genomes/hg38/bed/lastzGCF_009806435.1.2024-06-28
TMPDIR=/dev/shm

' > DEF

    time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \
       -qAsmId GCF_009806435.1_UM_NZW_1.0 -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
        -chainMinScore=3000 -chainLinearGap=medium) > do.log 2>&1
    grep -w real do.log | sed -e 's/^/    # /;'
    # real	440m44.908s

    sed -e 's/^/    # /;' fb.hg38.chainGCF_009806435.1Link.txt
    # 1338526147 bases of 3299210039 (40.571%) in intersection
    sed -e 's/^/    # /;' fb.hg38.chainSynGCF_009806435.1Link.txt
    # 1270488256 bases of 3299210039 (38.509%) in intersection

    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
       \
      -query2Bit="/hive/data/genomes/asmHubs/GCF/009/806/435/GCF_009806435.1/GCF_009806435.1.2bit" \
-querySizes="/hive/data/genomes/asmHubs/GCF/009/806/435/GCF_009806435.1/GCF_009806435.1.chrom.sizes.txt" \
        hg38 GCF_009806435.1) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	258m2.208s

    sed -e 's/^/    # /;' fb.hg38.chainRBest.GCF_009806435.1.txt
    # 1204430958 bases of 3299210039 (36.507%) in intersection

    ### and for the swap

    cd /hive/data/genomes/asmHubs/allBuild/GCF/009/806/435/GCF_009806435.1_UM_NZW_1.0/trackData/blastz.hg38.swap

   time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \
   -qAsmId GCF_009806435.1_UM_NZW_1.0 /hive/data/genomes/hg38/bed/lastzGCF_009806435.1.2024-06-28/DEF -swapDir=`pwd` \
  -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
    -chainMinScore=3000 -chainLinearGap=medium) > swap.log 2>&1

    grep -w real swap.log | sed -e 's/^/    # /;'
    # real	75m56.359s

    sed -e 's/^/    # /;' fb.GCF_009806435.1.chainHg38Link.txt
    # 1304799747 bases of 2841507030 (45.919%) in intersection
    sed -e 's/^/    # /;' fb.GCF_009806435.1.chainSynHg38Link.txt
    # 1234464415 bases of 2841507030 (43.444%) in intersection
\    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
    \
   -target2bit="/hive/data/genomes/asmHubs/GCF/009/806/435/GCF_009806435.1/GCF_009806435.1.2bit" \
-targetSizes="/hive/data/genomes/asmHubs/GCF/009/806/435/GCF_009806435.1/GCF_009806435.1.chrom.sizes.txt" \
   GCF_009806435.1 hg38) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	288m44.504s

    sed -e 's/^/    # /;' fb.GCF_009806435.1.chainRBest.Hg38.txt
    # 1206549303 bases of 2841507030 (42.462%) in intersection

real	1063m34.131s
user	0m2.848s
sys	0m3.184s

##############################################################################
# LASTZ Human Hg38 vs. domestic yak GCA_005887515.3
#    (DONE - 2024-09-03 - jairo)

    mkdir /hive/data/genomes/hg38/bed/lastzGCA_005887515.3.2024-09-03
    cd /hive/data/genomes/hg38/bed/lastzGCA_005887515.3.2024-09-03

    printf '# domestic yak GCA_005887515.3 vs. Human Hg38
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz

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

# QUERY: domestic yak 2019-06-10 GCA_005887515.3_BosGru3.1
SEQ2_DIR=/hive/data/genomes/asmHubs/GCA/005/887/515/GCA_005887515.3/GCA_005887515.3.2bit
SEQ2_LEN=/hive/data/genomes/asmHubs/GCA/005/887/515/GCA_005887515.3/GCA_005887515.3.chrom.sizes.txt
SEQ2_CHUNK=20000000
SEQ2_LAP=0
SEQ2_LIMIT=100

BASE=/hive/data/genomes/hg38/bed/lastzGCA_005887515.3.2024-09-03
TMPDIR=/dev/shm

' > DEF

    time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \
       -qAsmId GCA_005887515.3_BosGru3.1 -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
        -chainMinScore=3000 -chainLinearGap=medium) > do.log 2>&1
    grep -w real do.log | sed -e 's/^/    # /;'
    # real      518m35.100s

    sed -e 's/^/    # /;' fb.hg38.chainGCA_005887515.3Link.txt
    # 1392640940 bases of 3299210039 (42.211%) in intersection
    sed -e 's/^/    # /;' fb.hg38.chainSynGCA_005887515.3Link.txt
    # 1324979599 bases of 3299210039 (40.161%) in intersection

    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
       \
      -query2Bit="/hive/data/genomes/asmHubs/GCA/005/887/515/GCA_005887515.3/GCA_005887515.3.2bit" \
-querySizes="/hive/data/genomes/asmHubs/GCA/005/887/515/GCA_005887515.3/GCA_005887515.3.chrom.sizes.txt" \
        hg38 GCA_005887515.3) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real      305m47.663s

    sed -e 's/^/    # /;' fb.hg38.chainRBest.GCA_005887515.3.txt
    # 1246857312 bases of 3299210039 (37.793%) in intersection

    ### and for the swap

    cd /hive/data/genomes/asmHubs/allBuild/GCA/005/887/515/GCA_005887515.3_BosGru3.1/trackData/blastz.hg38.swap

   time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \
   -qAsmId GCA_005887515.3_BosGru3.1 /hive/data/genomes/hg38/bed/lastzGCA_005887515.3.2024-09-03/DEF -swapDir=`pwd` \
  -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
    -chainMinScore=3000 -chainLinearGap=medium) > swap.log 2>&1

    grep -w real swap.log | sed -e 's/^/    # /;'
    # real      81m25.155s

    sed -e 's/^/    # /;' fb.GCA_005887515.3.chainHg38Link.txt
    # 1394265201 bases of 2831460571 (49.242%) in intersection
    sed -e 's/^/    # /;' fb.GCA_005887515.3.chainSynHg38Link.txt
    # 1347828299 bases of 2831460571 (47.602%) in intersection
\    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
    \
   -target2bit="/hive/data/genomes/asmHubs/GCA/005/887/515/GCA_005887515.3/GCA_005887515.3.2bit" \
-targetSizes="/hive/data/genomes/asmHubs/GCA/005/887/515/GCA_005887515.3/GCA_005887515.3.chrom.sizes.txt" \
   GCA_005887515.3 hg38) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real      861m27.454s

    sed -e 's/^/    # /;' fb.GCA_005887515.3.chainRBest.Hg38.txt
    # 1250496047 bases of 2831460571 (44.164%) in intersection

##############################################################################
# LASTZ Human Hg38 vs. sugar glider GCA_028583685.1
#    (DONE - 2024-09-03 - jairo)

    mkdir /hive/data/genomes/hg38/bed/lastzGCA_028583685.1.2024-09-03
    cd /hive/data/genomes/hg38/bed/lastzGCA_028583685.1.2024-09-03

    printf '# sugar glider GCA_028583685.1 vs. Human Hg38
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz

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

# QUERY: sugar glider 2023-02-10 GCA_028583685.1_PetGlider_PUasm1.0
SEQ2_DIR=/hive/data/genomes/asmHubs/GCA/028/583/685/GCA_028583685.1/GCA_028583685.1.2bit
SEQ2_LEN=/hive/data/genomes/asmHubs/GCA/028/583/685/GCA_028583685.1/GCA_028583685.1.chrom.sizes.txt
SEQ2_CHUNK=20000000
SEQ2_LAP=0
SEQ2_LIMIT=100

BASE=/hive/data/genomes/hg38/bed/lastzGCA_028583685.1.2024-09-03
TMPDIR=/dev/shm

' > DEF

    time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \
       -qAsmId GCA_028583685.1_PetGlider_PUasm1.0 -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
        -chainMinScore=3000 -chainLinearGap=medium) > do.log 2>&1
    grep -w real do.log | sed -e 's/^/    # /;'
    # real      329m31.325s

    sed -e 's/^/    # /;' fb.hg38.chainGCA_028583685.1Link.txt
    # 254830797 bases of 3299210039 (7.724%) in intersection
    sed -e 's/^/    # /;' fb.hg38.chainSynGCA_028583685.1Link.txt
    # 109229739 bases of 3299210039 (3.311%) in intersection

    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
       \
      -query2Bit="/hive/data/genomes/asmHubs/GCA/028/583/685/GCA_028583685.1/GCA_028583685.1.2bit" \
-querySizes="/hive/data/genomes/asmHubs/GCA/028/583/685/GCA_028583685.1/GCA_028583685.1.chrom.sizes.txt" \
        hg38 GCA_028583685.1) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real      442m16.187s

    sed -e 's/^/    # /;' fb.hg38.chainRBest.GCA_028583685.1.txt
    # 214015545 bases of 3299210039 (6.487%) in intersection

    ### and for the swap

    cd /hive/data/genomes/asmHubs/allBuild/GCA/028/583/685/GCA_028583685.1_PetGlider_PUasm1.0/trackData/blastz.hg38.swap

   time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \
   -qAsmId GCA_028583685.1_PetGlider_PUasm1.0 /hive/data/genomes/hg38/bed/lastzGCA_028583685.1.2024-09-03/DEF -swapDir=`pwd` \
  -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
    -chainMinScore=3000 -chainLinearGap=medium) > swap.log 2>&1

    grep -w real swap.log | sed -e 's/^/    # /;'
    # real      24m48.018s

    sed -e 's/^/    # /;' fb.GCA_028583685.1.chainHg38Link.txt
    # 247775279 bases of 3464704272 (7.151%) in intersection
    sed -e 's/^/    # /;' fb.GCA_028583685.1.chainSynHg38Link.txt
    # 106375970 bases of 3464704272 (3.070%) in intersection
\    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
    \
   -target2bit="/hive/data/genomes/asmHubs/GCA/028/583/685/GCA_028583685.1/GCA_028583685.1.2bit" \
-targetSizes="/hive/data/genomes/asmHubs/GCA/028/583/685/GCA_028583685.1/GCA_028583685.1.chrom.sizes.txt" \
   GCA_028583685.1 hg38) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real      453m13.738s

    sed -e 's/^/    # /;' fb.GCA_028583685.1.chainRBest.Hg38.txt
    # 213968297 bases of 3464704272 (6.176%) in intersection

##############################################################################
##############################################################################
# LASTZ Human Hg38 vs. red deer GCF_910594005.1
#    (DONE - 2024-08-29 - jairo)

    mkdir /hive/data/genomes/hg38/bed/lastzGCF_910594005.1.2024-08-29
    cd /hive/data/genomes/hg38/bed/lastzGCF_910594005.1.2024-08-29

    printf '# red deer GCF_910594005.1 vs. Human Hg38
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz

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

# QUERY: red deer 2021-07-07 GCF_910594005.1_mCerEla1.1
SEQ2_DIR=/hive/data/genomes/asmHubs/GCF/910/594/005/GCF_910594005.1/GCF_910594005.1.2bit
SEQ2_LEN=/hive/data/genomes/asmHubs/GCF/910/594/005/GCF_910594005.1/GCF_910594005.1.chrom.sizes.txt
SEQ2_CHUNK=20000000
SEQ2_LAP=0
SEQ2_LIMIT=100

BASE=/hive/data/genomes/hg38/bed/lastzGCF_910594005.1.2024-08-29
TMPDIR=/dev/shm

' > DEF

    time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \
       -qAsmId GCF_910594005.1_mCerEla1.1 -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
        -chainMinScore=3000 -chainLinearGap=medium) > do.log 2>&1
    grep -w real do.log | sed -e 's/^/    # /;'
    # real      1617m14.834s

    sed -e 's/^/    # /;' fb.hg38.chainGCF_910594005.1Link.txt
    # 1462456359 bases of 3299210039 (44.327%) in intersection
    sed -e 's/^/    # /;' fb.hg38.chainSynGCF_910594005.1Link.txt
    # 1392968298 bases of 3299210039 (42.221%) in intersection

    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
       \
      -query2Bit="/hive/data/genomes/asmHubs/GCF/910/594/005/GCF_910594005.1/GCF_910594005.1.2bit" \
-querySizes="/hive/data/genomes/asmHubs/GCF/910/594/005/GCF_910594005.1/GCF_910594005.1.chrom.sizes.txt" \
        hg38 GCF_910594005.1) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real      257m51.239s

    sed -e 's/^/    # /;' fb.hg38.chainRBest.GCF_910594005.1.txt
    # 1307680530 bases of 3299210039 (39.636%) in intersection

    ### and for the swap

    cd /hive/data/genomes/asmHubs/allBuild/GCF/910/594/005/GCF_910594005.1_mCerEla1.1/trackData/blastz.hg38.swap

   time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \
   -qAsmId GCF_910594005.1_mCerEla1.1 /hive/data/genomes/hg38/bed/lastzGCF_910594005.1.2024-08-29/DEF -swapDir=`pwd` \
  -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
    -chainMinScore=3000 -chainLinearGap=medium) > swap.log 2>&1

    grep -w real swap.log | sed -e 's/^/    # /;'
    # real      99m46.211s

    sed -e 's/^/    # /;' fb.GCF_910594005.1.chainHg38Link.txt
    # 1388751208 bases of 2886603524 (48.110%) in intersection
    sed -e 's/^/    # /;' fb.GCF_910594005.1.chainSynHg38Link.txt
    # 1329736375 bases of 2886603524 (46.066%) in intersection
\    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
    \
   -target2bit="/hive/data/genomes/asmHubs/GCF/910/594/005/GCF_910594005.1/GCF_910594005.1.2bit" \
-targetSizes="/hive/data/genomes/asmHubs/GCF/910/594/005/GCF_910594005.1/GCF_910594005.1.chrom.sizes.txt" \
   GCF_910594005.1 hg38) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real      274m8.274s

    sed -e 's/^/    # /;' fb.GCF_910594005.1.chainRBest.Hg38.txt
    # 1308109027 bases of 2886603524 (45.317%) in intersection

##############################################################################
##############################################################################
# LASTZ Human Hg38 vs. sheep GCF_016772045.2
#    (DONE - 2024-08-29 - jairo)

    mkdir /hive/data/genomes/hg38/bed/lastzGCF_016772045.2.2024-08-29
    cd /hive/data/genomes/hg38/bed/lastzGCF_016772045.2.2024-08-29

    printf '# sheep GCF_016772045.2 vs. Human Hg38
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz

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

# QUERY: sheep 2023-07-20 GCF_016772045.2_ARS-UI_Ramb_v3.0
SEQ2_DIR=/hive/data/genomes/asmHubs/GCF/016/772/045/GCF_016772045.2/GCF_016772045.2.2bit
SEQ2_LEN=/hive/data/genomes/asmHubs/GCF/016/772/045/GCF_016772045.2/GCF_016772045.2.chrom.sizes.txt
SEQ2_CHUNK=20000000
SEQ2_LAP=0
SEQ2_LIMIT=100

BASE=/hive/data/genomes/hg38/bed/lastzGCF_016772045.2.2024-08-29
TMPDIR=/dev/shm

' > DEF

    time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \
       -qAsmId GCF_016772045.2_ARS-UI_Ramb_v3.0 -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
        -chainMinScore=3000 -chainLinearGap=medium) > do.log 2>&1
    grep -w real do.log | sed -e 's/^/    # /;'
    # real      765m43.186s

    sed -e 's/^/    # /;' fb.hg38.chainGCF_016772045.2Link.txt
    # 1427686356 bases of 3299210039 (43.274%) in intersection
    sed -e 's/^/    # /;' fb.hg38.chainSynGCF_016772045.2Link.txt
    # 1363288307 bases of 3299210039 (41.322%) in intersection

    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
       \
      -query2Bit="/hive/data/genomes/asmHubs/GCF/016/772/045/GCF_016772045.2/GCF_016772045.2.2bit" \
-querySizes="/hive/data/genomes/asmHubs/GCF/016/772/045/GCF_016772045.2/GCF_016772045.2.chrom.sizes.txt" \
        hg38 GCF_016772045.2) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real      282m27.955s

    sed -e 's/^/    # /;' fb.hg38.chainRBest.GCF_016772045.2.txt
    # 1280579203 bases of 3299210039 (38.815%) in intersection

    ### and for the swap

    cd /hive/data/genomes/asmHubs/allBuild/GCF/016/772/045/GCF_016772045.2_ARS-UI_Ramb_v3.0/trackData/blastz.hg38.swap

   time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \
   -qAsmId GCF_016772045.2_ARS-UI_Ramb_v3.0 /hive/data/genomes/hg38/bed/lastzGCF_016772045.2.2024-08-29/DEF -swapDir=`pwd` \
  -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
    -chainMinScore=3000 -chainLinearGap=medium) > swap.log 2>&1

    grep -w real swap.log | sed -e 's/^/    # /;'
    # real      75m52.789s

    sed -e 's/^/    # /;' fb.GCF_016772045.2.chainHg38Link.txt
    # 1329798265 bases of 2654063983 (50.104%) in intersection
    sed -e 's/^/    # /;' fb.GCF_016772045.2.chainSynHg38Link.txt
    # 1287911784 bases of 2654063983 (48.526%) in intersection
\    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
    \
   -target2bit="/hive/data/genomes/asmHubs/GCF/016/772/045/GCF_016772045.2/GCF_016772045.2.2bit" \
-targetSizes="/hive/data/genomes/asmHubs/GCF/016/772/045/GCF_016772045.2/GCF_016772045.2.chrom.sizes.txt" \
   GCF_016772045.2 hg38) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real      281m46.146s

    sed -e 's/^/    # /;' fb.GCF_016772045.2.chainRBest.Hg38.txt
    # 1281122070 bases of 2654063983 (48.270%) in intersection

##############################################################################
##############################################################################
# LASTZ Human Hg38 vs. Bactrian camel GCF_000767855.1
#    (DONE - 2024-08-29 - jairo)

    mkdir /hive/data/genomes/hg38/bed/lastzGCF_000767855.1.2024-08-29
    cd /hive/data/genomes/hg38/bed/lastzGCF_000767855.1.2024-08-29

    printf '# Bactrian camel GCF_000767855.1 vs. Human Hg38
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz

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

# QUERY: Bactrian camel 2014-10-23 GCF_000767855.1_Ca_bactrianus_MBC_1.0
SEQ2_DIR=/hive/data/genomes/asmHubs/GCF/000/767/855/GCF_000767855.1/GCF_000767855.1.2bit
SEQ2_LEN=/hive/data/genomes/asmHubs/GCF/000/767/855/GCF_000767855.1/GCF_000767855.1.chrom.sizes.txt
SEQ2_CHUNK=20000000
SEQ2_LAP=0
SEQ2_LIMIT=100

BASE=/hive/data/genomes/hg38/bed/lastzGCF_000767855.1.2024-08-29
TMPDIR=/dev/shm

' > DEF

    time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \
       -qAsmId GCF_000767855.1_Ca_bactrianus_MBC_1.0 -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
        -chainMinScore=3000 -chainLinearGap=medium) > do.log 2>&1
    grep -w real do.log | sed -e 's/^/    # /;'
    # real      759m53.919s

    sed -e 's/^/    # /;' fb.hg38.chainGCF_000767855.1Link.txt
    # 1536856108 bases of 3299210039 (46.583%) in intersection
    sed -e 's/^/    # /;' fb.hg38.chainSynGCF_000767855.1Link.txt
    # 1468539068 bases of 3299210039 (44.512%) in intersection

    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
       \
      -query2Bit="/hive/data/genomes/asmHubs/GCF/000/767/855/GCF_000767855.1/GCF_000767855.1.2bit" \
-querySizes="/hive/data/genomes/asmHubs/GCF/000/767/855/GCF_000767855.1/GCF_000767855.1.chrom.sizes.txt" \
        hg38 GCF_000767855.1) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real      182m17.263s

    sed -e 's/^/    # /;' fb.hg38.chainRBest.GCF_000767855.1.txt
    # 1372910494 bases of 3299210039 (41.613%) in intersection

    ### and for the swap

    cd /hive/data/genomes/asmHubs/allBuild/GCF/000/767/855/GCF_000767855.1_Ca_bactrianus_MBC_1.0/trackData/blastz.hg38.swap

   time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \
   -qAsmId GCF_000767855.1_Ca_bactrianus_MBC_1.0 /hive/data/genomes/hg38/bed/lastzGCF_000767855.1.2024-08-29/DEF -swapDir=`pwd` \
  -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
    -chainMinScore=3000 -chainLinearGap=medium) > swap.log 2>&1

    grep -w real swap.log | sed -e 's/^/    # /;'
    # real      81m24.949s

    sed -e 's/^/    # /;' fb.GCF_000767855.1.chainHg38Link.txt
    # 1409283773 bases of 1992663268 (70.724%) in intersection
    sed -e 's/^/    # /;' fb.GCF_000767855.1.chainSynHg38Link.txt
    # 1372565487 bases of 1992663268 (68.881%) in intersection
\    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
    \
   -target2bit="/hive/data/genomes/asmHubs/GCF/000/767/855/GCF_000767855.1/GCF_000767855.1.2bit" \
-targetSizes="/hive/data/genomes/asmHubs/GCF/000/767/855/GCF_000767855.1/GCF_000767855.1.chrom.sizes.txt" \
   GCF_000767855.1 hg38) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real      166m30.684s

    sed -e 's/^/    # /;' fb.GCF_000767855.1.chainRBest.Hg38.txt
    # 1373576819 bases of 1992663268 (68.932%) in intersection

##############################################################################
# LASTZ Human Hg38 vs. western European hedgehog GCF_950295315.1
#    (DONE - 2024-09-14 - Gerardo)

    mkdir /hive/data/genomes/hg38/bed/lastzGCF_950295315.1.2024-09-14
    cd /hive/data/genomes/hg38/bed/lastzGCF_950295315.1.2024-09-14

    printf '# western European hedgehog GCF_950295315.1 vs. Human Hg38
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz

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

# QUERY: western European hedgehog 2023-05-01 GCF_950295315.1_mEriEur2.1
SEQ2_DIR=/hive/data/genomes/asmHubs/GCF/950/295/315/GCF_950295315.1/GCF_950295315.1.2bit
SEQ2_LEN=/hive/data/genomes/asmHubs/GCF/950/295/315/GCF_950295315.1/GCF_950295315.1.chrom.sizes.txt
SEQ2_CHUNK=20000000
SEQ2_LAP=0
SEQ2_LIMIT=100

BASE=/hive/data/genomes/hg38/bed/lastzGCF_950295315.1.2024-09-14
TMPDIR=/dev/shm

' > DEF

    time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \
       -qAsmId GCF_950295315.1_mEriEur2.1 -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
        -chainMinScore=3000 -chainLinearGap=medium) > do.log 2>&1
    grep -w real do.log | sed -e 's/^/    # /;'
    # real	1070m35.939s

    sed -e 's/^/    # /;' fb.hg38.chainGCF_950295315.1Link.txt
    # 779724539 bases of 3299210039 (23.634%) in intersection
    sed -e 's/^/    # /;' fb.hg38.chainSynGCF_950295315.1Link.txt
    # 720598955 bases of 3299210039 (21.842%) in intersection

    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
       \
      -query2Bit="/hive/data/genomes/asmHubs/GCF/950/295/315/GCF_950295315.1/GCF_950295315.1.2bit" \
-querySizes="/hive/data/genomes/asmHubs/GCF/950/295/315/GCF_950295315.1/GCF_950295315.1.chrom.sizes.txt" \
        hg38 GCF_950295315.1) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	238m8.840s

    sed -e 's/^/    # /;' fb.hg38.chainRBest.GCF_950295315.1.txt
    # 695639959 bases of 3299210039 (21.085%) in intersection

    ### and for the swap

    cd /hive/data/genomes/asmHubs/allBuild/GCF/950/295/315/GCF_950295315.1_mEriEur2.1/trackData/blastz.hg38.swap

   time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \
   -qAsmId GCF_950295315.1_mEriEur2.1 /hive/data/genomes/hg38/bed/lastzGCF_950295315.1.2024-09-14/DEF -swapDir=`pwd` \
  -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
    -chainMinScore=3000 -chainLinearGap=medium) > swap.log 2>&1

    grep -w real swap.log | sed -e 's/^/    # /;'
    # real	49m21.433s

    sed -e 's/^/    # /;' fb.GCF_950295315.1.chainHg38Link.txt
    # 718540551 bases of 2720683831 (26.410%) in intersection
    sed -e 's/^/    # /;' fb.GCF_950295315.1.chainSynHg38Link.txt
    # 684033491 bases of 2720683831 (25.142%) in intersection
\    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
    \
   -target2bit="/hive/data/genomes/asmHubs/GCF/950/295/315/GCF_950295315.1/GCF_950295315.1.2bit" \
-targetSizes="/hive/data/genomes/asmHubs/GCF/950/295/315/GCF_950295315.1/GCF_950295315.1.chrom.sizes.txt" \
   GCF_950295315.1 hg38) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	222m21.349s

    sed -e 's/^/    # /;' fb.GCF_950295315.1.chainRBest.Hg38.txt
    # 696207129 bases of 2720683831 (25.589%) in intersection


real	1581m9.953s
user	0m4.705s
sys	0m20.521s
##############################################################################
# LASTZ Human Hg38 vs. domestic cattle GCF_002263795.3
#    (DONE - 2024-09-14 - Gerardo)

    mkdir /hive/data/genomes/hg38/bed/lastzGCF_002263795.3.2024-09-14
    cd /hive/data/genomes/hg38/bed/lastzGCF_002263795.3.2024-09-14

    printf '# domestic cattle GCF_002263795.3 vs. Human Hg38
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz

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

# QUERY: domestic cattle 2023-07-01 GCF_002263795.3_ARS-UCD2.0
SEQ2_DIR=/hive/data/genomes/asmHubs/GCF/002/263/795/GCF_002263795.3/GCF_002263795.3.2bit
SEQ2_LEN=/hive/data/genomes/asmHubs/GCF/002/263/795/GCF_002263795.3/GCF_002263795.3.chrom.sizes.txt
SEQ2_CHUNK=20000000
SEQ2_LAP=0
SEQ2_LIMIT=100

BASE=/hive/data/genomes/hg38/bed/lastzGCF_002263795.3.2024-09-14
TMPDIR=/dev/shm

' > DEF

    time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \
       -qAsmId GCF_002263795.3_ARS-UCD2.0 -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
        -chainMinScore=3000 -chainLinearGap=medium) > do.log 2>&1
    grep -w real do.log | sed -e 's/^/    # /;'
    # real	1360m45.921s

    sed -e 's/^/    # /;' fb.hg38.chainGCF_002263795.3Link.txt
    # 1437599863 bases of 3299210039 (43.574%) in intersection
    sed -e 's/^/    # /;' fb.hg38.chainSynGCF_002263795.3Link.txt
    # 1371275838 bases of 3299210039 (41.564%) in intersection

    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
       \
      -query2Bit="/hive/data/genomes/asmHubs/GCF/002/263/795/GCF_002263795.3/GCF_002263795.3.2bit" \
-querySizes="/hive/data/genomes/asmHubs/GCF/002/263/795/GCF_002263795.3/GCF_002263795.3.chrom.sizes.txt" \
        hg38 GCF_002263795.3) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	291m17.080s

    sed -e 's/^/    # /;' fb.hg38.chainRBest.GCF_002263795.3.txt
    # 1287906858 bases of 3299210039 (39.037%) in intersection

    ### and for the swap

    cd /hive/data/genomes/asmHubs/allBuild/GCF/002/263/795/GCF_002263795.3_ARS-UCD2.0/trackData/blastz.hg38.swap

   time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \
   -qAsmId GCF_002263795.3_ARS-UCD2.0 /hive/data/genomes/hg38/bed/lastzGCF_002263795.3.2024-09-14/DEF -swapDir=`pwd` \
  -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
    -chainMinScore=3000 -chainLinearGap=medium) > swap.log 2>&1

    grep -w real swap.log | sed -e 's/^/    # /;'
    # real	94m25.389s

    sed -e 's/^/    # /;' fb.GCF_002263795.3.chainHg38Link.txt
    # 1351306335 bases of 2770686120 (48.772%) in intersection
    sed -e 's/^/    # /;' fb.GCF_002263795.3.chainSynHg38Link.txt
    # 1304221756 bases of 2770686120 (47.072%) in intersection
\    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
    \
   -target2bit="/hive/data/genomes/asmHubs/GCF/002/263/795/GCF_002263795.3/GCF_002263795.3.2bit" \
-targetSizes="/hive/data/genomes/asmHubs/GCF/002/263/795/GCF_002263795.3/GCF_002263795.3.chrom.sizes.txt" \
   GCF_002263795.3 hg38) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	309m22.281s

    sed -e 's/^/    # /;' fb.GCF_002263795.3.chainRBest.Hg38.txt
    # 1288620776 bases of 2770686120 (46.509%) in intersection

real	2055m58.482s
user	0m3.619s
sys	0m9.300s
##############################################################################
# LASTZ Human Hg38 vs. dog GCF_011100685.1
#    (DONE - 2024-09-14 - Gerardo)

    mkdir /hive/data/genomes/hg38/bed/lastzGCF_011100685.1.2024-09-14
    cd /hive/data/genomes/hg38/bed/lastzGCF_011100685.1.2024-09-14

    printf '# dog GCF_011100685.1 vs. Human Hg38
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz

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

# QUERY: dog 2020-03-10 GCF_011100685.1_UU_Cfam_GSD_1.0
SEQ2_DIR=/hive/data/genomes/asmHubs/GCF/011/100/685/GCF_011100685.1/GCF_011100685.1.2bit
SEQ2_LEN=/hive/data/genomes/asmHubs/GCF/011/100/685/GCF_011100685.1/GCF_011100685.1.chrom.sizes.txt
SEQ2_CHUNK=20000000
SEQ2_LAP=0
SEQ2_LIMIT=100

BASE=/hive/data/genomes/hg38/bed/lastzGCF_011100685.1.2024-09-14
TMPDIR=/dev/shm

' > DEF

    time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \
       -qAsmId GCF_011100685.1_UU_Cfam_GSD_1.0 -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
        -chainMinScore=3000 -chainLinearGap=medium) > do.log 2>&1
    grep -w real do.log | sed -e 's/^/    # /;'
    # real	1637m0.994s

    sed -e 's/^/    # /;' fb.hg38.chainGCF_011100685.1Link.txt
    # 1588231052 bases of 3299210039 (48.140%) in intersection
    sed -e 's/^/    # /;' fb.hg38.chainSynGCF_011100685.1Link.txt
    # 1521346162 bases of 3299210039 (46.112%) in intersection

    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
       \
      -query2Bit="/hive/data/genomes/asmHubs/GCF/011/100/685/GCF_011100685.1/GCF_011100685.1.2bit" \
-querySizes="/hive/data/genomes/asmHubs/GCF/011/100/685/GCF_011100685.1/GCF_011100685.1.chrom.sizes.txt" \
        hg38 GCF_011100685.1) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	281m48.990s

    sed -e 's/^/    # /;' fb.hg38.chainRBest.GCF_011100685.1.txt
    # 1425161610 bases of 3299210039 (43.197%) in intersection

    ### and for the swap

    cd /hive/data/genomes/asmHubs/allBuild/GCF/011/100/685/GCF_011100685.1_UU_Cfam_GSD_1.0/trackData/blastz.hg38.swap

   time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \
   -qAsmId GCF_011100685.1_UU_Cfam_GSD_1.0 /hive/data/genomes/hg38/bed/lastzGCF_011100685.1.2024-09-14/DEF -swapDir=`pwd` \
  -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
    -chainMinScore=3000 -chainLinearGap=medium) > swap.log 2>&1

    grep -w real swap.log | sed -e 's/^/    # /;'
    # real	125m45.802s

    sed -e 's/^/    # /;' fb.GCF_011100685.1.chainHg38Link.txt
    # 1492725079 bases of 2481983352 (60.142%) in intersection
    sed -e 's/^/    # /;' fb.GCF_011100685.1.chainSynHg38Link.txt
    # 1447552241 bases of 2481983352 (58.322%) in intersection
\    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
    \
   -target2bit="/hive/data/genomes/asmHubs/GCF/011/100/685/GCF_011100685.1/GCF_011100685.1.2bit" \
-targetSizes="/hive/data/genomes/asmHubs/GCF/011/100/685/GCF_011100685.1/GCF_011100685.1.chrom.sizes.txt" \
   GCF_011100685.1 hg38) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	255m23.446s

    sed -e 's/^/    # /;' fb.GCF_011100685.1.chainRBest.Hg38.txt
    # 1425408450 bases of 2481983352 (57.430%) in intersection

real	2300m12.938s
user	0m2.731s
sys	0m12.713s
##############################################################################
# LASTZ Human Hg38 vs. white-tufted-ear marmoset GCA_011100555.2
#    (DONE - 2024-11-22 - mspeir)

    mkdir /hive/data/genomes/hg38/bed/lastzGCA_011100555.2.2024-11-22
    cd /hive/data/genomes/hg38/bed/lastzGCA_011100555.2.2024-11-22

    printf '# white-tufted-ear marmoset GCA_011100555.2 vs. Human Hg38
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz
BLASTZ_T=2
BLASTZ_O=600
BLASTZ_E=150
BLASTZ_M=254
BLASTZ_K=4500
BLASTZ_Y=15000
BLASTZ_Q=/hive/data/staging/data/blastz/human_chimp.v2.q
#       A     C     G     T
# A    90  -330  -236  -356
# C  -330   100  -318  -236
# G  -236  -318   100  -330
# T  -356  -236  -330    90

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

# QUERY: white-tufted-ear marmoset 2021-04-28 GCA_011100555.2_mCalJa1.2.pat.X
SEQ2_DIR=/hive/data/genomes/asmHubs/GCA/011/100/555/GCA_011100555.2/GCA_011100555.2.2bit
SEQ2_LEN=/hive/data/genomes/asmHubs/GCA/011/100/555/GCA_011100555.2/GCA_011100555.2.chrom.sizes.txt
SEQ2_CHUNK=20000000
SEQ2_LAP=0
SEQ2_LIMIT=100

BASE=/hive/data/genomes/hg38/bed/lastzGCA_011100555.2.2024-11-22
TMPDIR=/dev/shm

' > DEF

    time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \
       -qAsmId GCA_011100555.2_mCalJa1.2.pat.X -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=hgwdev \
        -chainMinScore=5000 -chainLinearGap=medium) > do.log 2>&1
    grep -w real do.log | sed -e 's/^/    # /;'
    # real	118m17.235s

    sed -e 's/^/    # /;' fb.hg38.chainGCA_011100555.2Link.txt
    # 2189250745 bases of 3299210039 (66.357%) in intersection
    sed -e 's/^/    # /;' fb.hg38.chainSynGCA_011100555.2Link.txt
    # 2148028479 bases of 3299210039 (65.107%) in intersection

    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
       \
      -query2Bit="/hive/data/genomes/asmHubs/GCA/011/100/555/GCA_011100555.2/GCA_011100555.2.2bit" \
-querySizes="/hive/data/genomes/asmHubs/GCA/011/100/555/GCA_011100555.2/GCA_011100555.2.chrom.sizes.txt" \
        hg38 GCA_011100555.2) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	149m56.908s

    sed -e 's/^/    # /;' fb.hg38.chainRBest.GCA_011100555.2.txt
    # 1999972943 bases of 3299210039 (60.620%) in intersection

real	562m50.862s
user	0m6.353s
sys	0m4.283s

##############################################################################
# LASTZ Human Hg38 vs. olive baboon GCF_008728515.1
#    (DONE - 2024-11-22 - mspeir)

    mkdir /hive/data/genomes/hg38/bed/lastzGCF_008728515.1.2023-08-31
    cd /hive/data/genomes/hg38/bed/lastzGCF_008728515.1.2023-08-31

    printf '# olive baboon GCF_008728515.1 vs. Human Hg38
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz
BLASTZ_T=2
BLASTZ_O=600
BLASTZ_E=150
BLASTZ_M=254
BLASTZ_K=4500
BLASTZ_Y=15000
BLASTZ_Q=/hive/data/staging/data/blastz/human_chimp.v2.q
#       A     C     G     T
# A    90  -330  -236  -356
# C  -330   100  -318  -236
# G  -236  -318   100  -330
# T  -356  -236  -330    90

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

# QUERY: olive baboon 2019-10-02 GCF_008728515.1_Panubis1.0
SEQ2_DIR=/hive/data/genomes/asmHubs/GCF/008/728/515/GCF_008728515.1/GCF_008728515.1.2bit
SEQ2_LEN=/hive/data/genomes/asmHubs/GCF/008/728/515/GCF_008728515.1/GCF_008728515.1.chrom.sizes.txt
SEQ2_CHUNK=20000000
SEQ2_LAP=0
SEQ2_LIMIT=100

BASE=/hive/data/genomes/hg38/bed/lastzGCF_008728515.1.2023-08-31
TMPDIR=/dev/shm

' > DEF

    time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \
       -qAsmId GCF_008728515.1_Panubis1.0 -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=hgwdev \
        -chainMinScore=5000 -chainLinearGap=medium) > do.log 2>&1
    grep -w real do.log | sed -e 's/^/    # /;'
    # real	111m16.100s

    sed -e 's/^/    # /;' fb.hg38.chainGCF_008728515.1Link.txt
    # 2638181355 bases of 3299210039 (79.964%) in intersection
    sed -e 's/^/    # /;' fb.hg38.chainSynGCF_008728515.1Link.txt
    # 2586288619 bases of 3299210039 (78.391%) in intersection

    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
       \
      -query2Bit="/hive/data/genomes/asmHubs/GCF/008/728/515/GCF_008728515.1/GCF_008728515.1.2bit" \
-querySizes="/hive/data/genomes/asmHubs/GCF/008/728/515/GCF_008728515.1/GCF_008728515.1.chrom.sizes.txt" \
        hg38 GCF_008728515.1) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	109m19.490s

    sed -e 's/^/    # /;' fb.hg38.chainRBest.GCF_008728515.1.txt
    # 2400768727 bases of 3299210039 (72.768%) in intersection

real	0m0.402s
user	0m0.087s
sys	0m0.154s

##############################################################################
# LASTZ Human Hg38 vs. sooty mangabey GCF_000955945.1
#    (DONE - 2024-11-24 - mspeir)

    mkdir /hive/data/genomes/hg38/bed/lastzGCF_000955945.1.2024-11-24
    cd /hive/data/genomes/hg38/bed/lastzGCF_000955945.1.2024-11-24

    printf '# sooty mangabey GCF_000955945.1 vs. Human Hg38
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz
BLASTZ_T=2
BLASTZ_O=600
BLASTZ_E=150
BLASTZ_M=254
BLASTZ_K=4500
BLASTZ_Y=15000
BLASTZ_Q=/hive/data/staging/data/blastz/human_chimp.v2.q
#       A     C     G     T
# A    90  -330  -236  -356
# C  -330   100  -318  -236
# G  -236  -318   100  -330
# T  -356  -236  -330    90

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

# QUERY: sooty mangabey 2015-03-19 GCF_000955945.1_Caty_1.0
SEQ2_DIR=/hive/data/genomes/asmHubs/GCF/000/955/945/GCF_000955945.1/GCF_000955945.1.2bit
SEQ2_LEN=/hive/data/genomes/asmHubs/GCF/000/955/945/GCF_000955945.1/GCF_000955945.1.chrom.sizes.txt
SEQ2_CHUNK=20000000
SEQ2_LAP=0
SEQ2_LIMIT=100

BASE=/hive/data/genomes/hg38/bed/lastzGCF_000955945.1.2024-11-24
TMPDIR=/dev/shm

' > DEF

    time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \
       -qAsmId GCF_000955945.1_Caty_1.0 -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=hgwdev \
        -chainMinScore=5000 -chainLinearGap=medium) > do.log 2>&1
    grep -w real do.log | sed -e 's/^/    # /;'
    # real	140m41.682s

    sed -e 's/^/    # /;' fb.hg38.chainGCF_000955945.1Link.txt
    # 2627114328 bases of 3299210039 (79.629%) in intersection
    sed -e 's/^/    # /;' fb.hg38.chainSynGCF_000955945.1Link.txt
    # 2580198826 bases of 3299210039 (78.207%) in intersection

    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
       \
      -query2Bit="/hive/data/genomes/asmHubs/GCF/000/955/945/GCF_000955945.1/GCF_000955945.1.2bit" \
-querySizes="/hive/data/genomes/asmHubs/GCF/000/955/945/GCF_000955945.1/GCF_000955945.1.chrom.sizes.txt" \
        hg38 GCF_000955945.1) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	104m0.149s

    sed -e 's/^/    # /;' fb.hg38.chainRBest.GCF_000955945.1.txt
    # 2383807464 bases of 3299210039 (72.254%) in intersection

real	467m35.051s
user	0m6.086s
sys	0m4.122s

##############################################################################
# LASTZ Human Hg38 vs. pig-tailed macaque GCF_000956065.1
#    (DONE - 2024-11-24 - mspeir)

    mkdir /hive/data/genomes/hg38/bed/lastzGCF_000956065.1.2024-11-24
    cd /hive/data/genomes/hg38/bed/lastzGCF_000956065.1.2024-11-24

    printf '# pig-tailed macaque GCF_000956065.1 vs. Human Hg38
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz
BLASTZ_T=2
BLASTZ_O=600
BLASTZ_E=150
BLASTZ_M=254
BLASTZ_K=4500
BLASTZ_Y=15000
BLASTZ_Q=/hive/data/staging/data/blastz/human_chimp.v2.q
#       A     C     G     T
# A    90  -330  -236  -356
# C  -330   100  -318  -236
# G  -236  -318   100  -330
# T  -356  -236  -330    90

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

# QUERY: pig-tailed macaque 2015-03-19 GCF_000956065.1_Mnem_1.0
SEQ2_DIR=/hive/data/genomes/asmHubs/GCF/000/956/065/GCF_000956065.1/GCF_000956065.1.2bit
SEQ2_LEN=/hive/data/genomes/asmHubs/GCF/000/956/065/GCF_000956065.1/GCF_000956065.1.chrom.sizes.txt
SEQ2_CHUNK=20000000
SEQ2_LAP=0
SEQ2_LIMIT=100

BASE=/hive/data/genomes/hg38/bed/lastzGCF_000956065.1.2024-11-24
TMPDIR=/dev/shm

' > DEF

    time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \
       -qAsmId GCF_000956065.1_Mnem_1.0 -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=hgwdev \
        -chainMinScore=5000 -chainLinearGap=medium) > do.log 2>&1
    grep -w real do.log | sed -e 's/^/    # /;'
    # real	140m45.442s

    sed -e 's/^/    # /;' fb.hg38.chainGCF_000956065.1Link.txt
    # 2617335207 bases of 3299210039 (79.332%) in intersection
    sed -e 's/^/    # /;' fb.hg38.chainSynGCF_000956065.1Link.txt
    # 2559419006 bases of 3299210039 (77.577%) in intersection

    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
       \
      -query2Bit="/hive/data/genomes/asmHubs/GCF/000/956/065/GCF_000956065.1/GCF_000956065.1.2bit" \
-querySizes="/hive/data/genomes/asmHubs/GCF/000/956/065/GCF_000956065.1/GCF_000956065.1.chrom.sizes.txt" \
        hg38 GCF_000956065.1) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	102m13.608s

    sed -e 's/^/    # /;' fb.hg38.chainRBest.GCF_000956065.1.txt
    # 2376330049 bases of 3299210039 (72.027%) in intersection

real	471m16.938s
user	0m6.847s
sys	0m3.999s

##############################################################################
# LASTZ Human Hg38 vs. dog GCF_014441545.1
#    (DONE - 2024-11-24 - mspeir)

    mkdir /hive/data/genomes/hg38/bed/lastzGCF_014441545.1.2024-11-24
    cd /hive/data/genomes/hg38/bed/lastzGCF_014441545.1.2024-11-24

    printf '# dog GCF_014441545.1 vs. Human Hg38
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz

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

# QUERY: dog 2020-09-03 GCF_014441545.1_ROS_Cfam_1.0
SEQ2_DIR=/hive/data/genomes/asmHubs/GCF/014/441/545/GCF_014441545.1/GCF_014441545.1.2bit
SEQ2_LEN=/hive/data/genomes/asmHubs/GCF/014/441/545/GCF_014441545.1/GCF_014441545.1.chrom.sizes.txt
SEQ2_CHUNK=20000000
SEQ2_LAP=0
SEQ2_LIMIT=100

BASE=/hive/data/genomes/hg38/bed/lastzGCF_014441545.1.2024-11-24
TMPDIR=/dev/shm

' > DEF

    time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \
       -qAsmId GCF_014441545.1_ROS_Cfam_1.0 -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=hgwdev \
        -chainMinScore=3000 -chainLinearGap=medium) > do.log 2>&1
    grep -w real do.log | sed -e 's/^/    # /;'
    # real	518m26.232s

    sed -e 's/^/    # /;' fb.hg38.chainGCF_014441545.1Link.txt
    # 1585328629 bases of 3299210039 (48.052%) in intersection
    sed -e 's/^/    # /;' fb.hg38.chainSynGCF_014441545.1Link.txt
    # 1518416772 bases of 3299210039 (46.024%) in intersection

    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
       \
      -query2Bit="/hive/data/genomes/asmHubs/GCF/014/441/545/GCF_014441545.1/GCF_014441545.1.2bit" \
-querySizes="/hive/data/genomes/asmHubs/GCF/014/441/545/GCF_014441545.1/GCF_014441545.1.chrom.sizes.txt" \
        hg38 GCF_014441545.1) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	252m7.964s

    sed -e 's/^/    # /;' fb.hg38.chainRBest.GCF_014441545.1.txt

real	1208m0.275s
user	0m2.919s
sys	0m3.733s
