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# LASTZ Zebrafish DanRer11 vs. D. melanogaster Dm6
#    (DONE - 2022-09-13 - hiram)
# per user request redmine #29981

    mkdir /hive/data/genomes/danRer11/bed/lastzDm6.2022-09-13
    cd /hive/data/genomes/danRer11/bed/lastzDm6.2022-09-13

    printf '# D. melanogaster Dm6 vs. Zebrafish DanRer11
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz

# TARGET: Zebrafish  danRer11
SEQ1_DIR=/hive/data/genomes/danRer11/danRer11.2bit
SEQ1_LEN=/hive/data/genomes/danRer11/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
SEQ1_LIMIT=40

# QUERY: D. melanogaster  dm6
SEQ2_DIR=/hive/data/genomes/dm6/dm6.2bit
SEQ2_LEN=/hive/data/genomes/dm6/chrom.sizes
SEQ2_CHUNK=20000000
SEQ2_LAP=0
SEQ2_LIMIT=100

BASE=/hive/data/genomes/danRer11/bed/lastzDm6.2022-09-13
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=loose) > do.log 2>&1
    grep -w real do.log | sed -e 's/^/    # /;'
    # real	13m28.637s

    sed -e 's/^/    # /;' fb.danRer11.chainDm6Link.txt
    # 9922943 bases of 1674677181 (0.593%) in intersection
    sed -e 's/^/    # /;' fb.danRer11.chainSynDm6Link.txt
    # 65331 bases of 1674677181 (0.004%) in intersection

    time (~/kent/src/hg/utils/automation/doRecipBest.pl  -load -workhorse=hgwdev -buildDir=`pwd` \
       \
       \
        danRer11 dm6) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	11m31.879s

    sed -e 's/^/    # /;' fb.danRer11.chainRBest.Dm6.txt
    # 3483314 bases of 1674677181 (0.208%) in intersection

    ### and for the swap

    cd /hive/data/genomes/dm6/bed/blastz.danRer11.swap

   time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl  -swap -verbose=2 \
    /hive/data/genomes/danRer11/bed/lastzDm6.2022-09-13/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	1m12.711s

    sed -e 's/^/    # /;' fb.dm6.chainDanRer11Link.txt
    # 4086744 bases of 142573024 (2.866%) in intersection
    sed -e 's/^/    # /;' fb.dm6.chainSynDanRer11Link.txt
    # 42241 bases of 142573024 (0.030%) in intersection
\    time (~/kent/src/hg/utils/automation/doRecipBest.pl  -load -workhorse=hgwdev -buildDir=`pwd` \
    \
    \
   dm6 danRer11) > rbest.log 2>&1

    grep -w real rbest.log | sed -e 's/^/    # /;'
    # real	8m35.092s

    sed -e 's/^/    # /;' fb.dm6.chainRBest.DanRer11.txt
    # 3396581 bases of 142573024 (2.382%) in intersection

real	34m48.592s
user	0m0.866s
sys	0m0.812s
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