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

# This file describes browser build for the droSim2
# Organism name:  Drosophila simulans

#  Must find the photograph first, can not continue until finding
#  the photograph.

#########################################################################
#  Initial steps, find photograph (DONE - 2016-11-01 - Hiram)

# To start this initialBuild.txt document, from a previous assembly document:

mkdir ~/kent/src/hg/makeDb/doc/droSim2
cd ~/kent/src/hg/makeDb/doc/droSim2

sed -e 's/gorGor5/droSim2/g; s/GorGor5/DroSim2/g; s/TBD/TBD/g;' ../gorGor5/initialBuild.txt > initialBuild.txt

mkdir -p /hive/data/genomes/droSim2/refseq
cd /hive/data/genomes/droSim2/refseq

rsync -a -P -L \
rsync://ftp.ncbi.nlm.nih.gov/genomes/refseq/invertebrate/Drosophila_simulans/all_assembly_versions/GCF_000754195.2_ASM75419v2/ ./

# obtain photo from wikimedia commons
mkdir /hive/data/genomes/droSim2/photograph
cd /hive/data/genomes/droSim2/photograph
wget --timestamping \
https://upload.wikimedia.org/wikipedia/commons/0/03/Drosophila_simulans-female.jpg

cd /hive/data/genomes/droSim2
printf "photoCreditURL https://commons.wikimedia.org/wiki/File:Drosophila_simulans-female.jpg
photoCreditName Wikimedia Commons/Dr. Andrew Weeks\n" > photoReference.txt

# this information is from the top of 
#    refseq/*_assembly_report.txt
#    (aka: refseq/GCF_000754195.2_ASM75419v2_assembly_report.txt)

# Assembly name:  ASM75419v2
# Organism name:  Drosophila simulans (flies)
# Infraspecific name:  strain=w501
# Taxid:          7240
# BioSample:      SAMN01086904
# BioProject:     PRJNA297806
# Submitter:      Princeton University
# Date:           2014-9-19
# Assembly type:  haploid
# Release type:   
# Assembly level: Chromosome
# Genome representation: full
# WGS project:    JPYS01
# Assembly method: Velvet v. 1.1.04
# Expected final version: No
# Genome coverage: 75.0x
# Sequencing technology: Illumina; Sanger
# RefSeq category: Representative Genome
# GenBank assembly accession: GCA_000754195.2
# RefSeq assembly accession: GCF_000754195.2
# RefSeq assembly and GenBank assemblies identical: no
#
## Assembly-Units:
## GenBank Unit Accession       RefSeq Unit Accession   Assembly-Unit name
## GCA_000754205.2      GCF_000754205.1 Primary Assembly
## GCA_000754215.1      GCF_000045355.1 non-nuclear


#############################################################################
# establish config.ra file (DONE - Hiram - 2016-11-01)
    cd /hive/data/genomes/droSim2
    /cluster/home/hiram/kent/src/hg/utils/automation/prepConfig.pl \
  droSim2 insect drosophila ./refseq/*_assembly_report.txt

# change commonName "Flies" to "D. simulans"

    # verify it looks sane
    cat droSim2.config.ra
# config parameters for makeGenomeDb.pl:
db droSim2
clade insect
genomeCladePriority 70
scientificName Drosophila simulans
commonName D. simulans
assemblyDate Sep. 2014
assemblyLabel Princeton University
assemblyShortLabel ASM75419v2
orderKey 6684
# mitochondrial sequence included in refseq release
# mitoAcc NC_005781.1
mitoAcc none
fastaFiles /hive/data/genomes/droSim2/ucsc/*.fa.gz
agpFiles /hive/data/genomes/droSim2/ucsc/*.agp
# qualFiles none
dbDbSpeciesDir drosophila
photoCreditURL https://commons.wikimedia.org/wiki/File:Drosophila_simulans-female.jpg
photoCreditName Wikimedia Commons/Dr. Andrew Weeks
ncbiGenomeId 200
ncbiAssemblyId 800241
ncbiAssemblyName ASM75419v2
ncbiBioProject 297806
ncbiBioSample SAMN01086904
genBankAccessionID GCF_000754195.2
taxId 7240

#############################################################################
# setup UCSC named files (DONE - 2016-11-01 - Hiram)

    mkdir /hive/data/genomes/droSim2/ucsc
    cd /hive/data/genomes/droSim2/ucsc
    # measure what is in the genbank release:
    faSize ../refseq/G*2_genomic.fna.gz
# 124963774 bases (378345 N's 124585429 real 98768053 upper 25817376 lower)
#   in 7619 sequences in 1 files
# Total size: mean 16401.6 sd 603260.6 min 200 (NW_015503630.1)
#   max 27160941 (NT_479536.1) median 320
# %20.66 masked total, %20.72 masked real

    # check for duplicate sequences, twoBitDup should be silent output:

    faToTwoBit -noMask ../refseq/*2_genomic.fna.gz refseq.2bit
    twoBitDup refseq.2bit
    # no output is a good result, otherwise, would have to eliminate duplicates

    ~/kent/src/hg/utils/automation/ucscCompositeAgp.pl \
      ../refseq/*2_genomic.fna.gz \
         ../refseq/*_assembly_structure/Primary_Assembly
    # real    0m43.539s

    ~/kent/src/hg/utils/automation/unplacedWithChroms.pl \
       ../refseq/*_assembly_structure/Primary_Assembly

    ~/kent/src/hg/utils/automation/unlocalizedWithChroms.pl \
       ../refseq/*_assembly_structure/Primary_Assembly
    # real    0m57.496s  (two steps above)

    export mitoAcc=`grep "^# mitoAcc" ../droSim2.config.ra | awk '{print $NF}'`
    printf "# mitoAcc %s\n" "$mitoAcc"

 zcat ../refseq/*_assembly_structure/non-nuclear/assem*/AGP/chrMT.comp.agp.gz \
     | grep -v "^#" | sed -e "s/^$mitoAcc/chrM/;" > chrM.agp

    printf ">chrM\n" > chrM.fa
    twoBitToFa -noMask refseq.2bit:$mitoAcc stdout | grep -v "^>" >> chrM.fa
    gzip chrM.fa


    faToTwoBit *.fa.gz test.2bit
    twoBitDup test.2bit
    cat *.agp | checkAgpAndFa stdin test.2bit 2>&1 | tail -4

    # no longer need the 2bit files
    rm refseq.2bit test.2bit

#############################################################################
#  Initial database build (DONE - 2016-11-01 - Hiram)

    # verify sequence and AGP are OK:
    cd /hive/data/genomes/droSim2

    time (makeGenomeDb.pl -workhorse=hgwdev -dbHost=hgwdev -fileServer=hgwdev \
         droSim2.config.ra) > makeGenomeDb.log
    # real    1m43.905s

    # check in the trackDb files created and add to trackDb/makefile

##############################################################################
# cpgIslands on UNMASKED sequence (DONE - 2016-11-02 - Hiram)
    mkdir /hive/data/genomes/droSim2/bed/cpgIslandsUnmasked
    cd /hive/data/genomes/droSim2/bed/cpgIslandsUnmasked

    time (doCpgIslands.pl -dbHost=hgwdev -bigClusterHub=ku -buildDir=`pwd` \
       -tableName=cpgIslandExtUnmasked \
          -maskedSeq=/hive/data/genomes/droSim2/droSim2.unmasked.2bit \
             -workhorse=hgwdev -smallClusterHub=ku droSim2) > do.log 2>&1
    # real    2m17.187s

    cat fb.droSim2.cpgIslandExtUnmasked.txt
    # 21753930 bases of 124963774 (17.408%) in intersection

#############################################################################
# cytoBandIdeo - (DONE - 2016-11-01 - Hiram)
    mkdir /hive/data/genomes/droSim2/bed/cytoBand
    cd /hive/data/genomes/droSim2/bed/cytoBand
    makeCytoBandIdeo.csh droSim2

#############################################################################
# ucscToINSDC table/track (TBD - 2016-08-05 - Hiram)
    # there are no other names for contigs in this assembly, there are just
    # the contig names

#########################################################################
# fixup search rule for assembly track/gold table (TBD - 2016-08-05 - Hiram)

    cd ~/kent/src/hg/makeDb/trackDb/gorilla/droSim2
    # preview prefixes and suffixes:
    hgsql -N -e "select frag from gold;" droSim2 \
      | sed -e 's/[0-9][0-9]*//;' | sort | uniq -c 
#    15997 CYUIv1_1
#        1 LN.1

    # implies a search rule of: '[CILNUY0-9]+([v0-9_\.]+)?'

    # verify this rule will find them all or eliminate them all:
    hgsql -N -e "select frag from gold;" droSim2 | wc -l
    # 15998

    hgsql -N -e "select frag from gold;" droSim2 \
       | egrep -e '[CILNUY0-9]+([v0-9_\.]+)?' | wc -l
    # 15998

    hgsql -N -e "select frag from gold;" droSim2 \
       | egrep -v -e '[CILNUY0-9]+([v0-9_\.]+)?' | wc -l
    # 0

    # hence, add to trackDb/rhesus/droSim2/trackDb.ra
searchTable gold
shortCircuit 1
termRegex [CILNUY0-9]+([v0-9_\.]+)?
query select chrom,chromStart,chromEnd,frag from %s where frag like '%s%%'
searchPriority 8

    # verify searches work in the position box

##########################################################################
# running repeat masker (DONE - 2016-11-01 - Hiram)
    mkdir /hive/data/genomes/droSim2/bed/repeatMasker
    cd /hive/data/genomes/droSim2/bed/repeatMasker
    # failed to create a log file, made mistake
    doRepeatMasker.pl -buildDir=`pwd` \
        -bigClusterHub=ku -dbHost=hgwdev -workhorse=hgwdev \
        -smallClusterHub=ku droSim2
    # real    1581m32.299s

    cat faSize.rmsk.txt
# 124963774 bases (378345 N's 124585429 real 111673206 upper 12912223 lower)
#    in 7619 sequences in 1 files
# Total size: mean 16401.6 sd 603260.6 min 200 (chrUn_NW_015503630v1)
#    max 27160941 (chr3R) median 320
# %10.33 masked total, %10.36 masked real

    egrep -i "versi|relea" do.log
    # RepeatMasker version open-4.0.5
    # Search Engine: Crossmatch [ 1.090518 ]
    # Master RepeatMasker Database: /hive/data/staging/data/RepeatMasker140131/Libraries/RepeatMaskerLib.embl ( Complete Database: 20140131 )

    # RepeatMasker version open-4.0.5
    #    January 31 2015 (open-4-0-5) version of RepeatMasker
    # CC   RELEASE 20140131;

    time featureBits -countGaps droSim2 rmsk
    # 12951235 bases of 124963774 (10.364%) in intersection
    # real    0m3.712s

    # with high contig count assemblies, faster way to get the same result:
    time hgsql -N -e 'select genoName,genoStart,genoEnd from rmsk;' droSim2 \
        | bedSingleCover.pl stdin | ave -col=4 stdin | grep "^total"
    # total 12951235.000000
    # real    0m0.852s

##########################################################################
# running simple repeat (DONE - 2016-11-01 - Hiram)

    mkdir /hive/data/genomes/droSim2/bed/simpleRepeat
    cd /hive/data/genomes/droSim2/bed/simpleRepeat
    time (doSimpleRepeat.pl -buildDir=`pwd` -bigClusterHub=ku \
        -trf409=6 -dbHost=hgwdev -workhorse=hgwdev -smallClusterHub=ku \
        droSim2) > do.log 2>&1
    # real    6m32.563s

    cat fb.simpleRepeat
    # 1545440 bases of 124963774 (1.237%) in intersection

    # add to window masker result after it is done:
    cd /hive/data/genomes/droSim2
    twoBitMask bed/windowMasker/droSim2.cleanWMSdust.2bit \
        -add bed/simpleRepeat/trfMask.bed droSim2.2bit
    #   you can safely ignore the warning about fields >= 13
    twoBitToFa droSim2.2bit stdout | faSize stdin > faSize.droSim2.2bit.txt
    cat faSize.droSim2.2bit.txt
# 124963774 bases (378345 N's 124585429 real 97540956 upper 27044473 lower)
#    in 7619 sequences in 1 files
# Total size: mean 16401.6 sd 603260.6 min 200 (chrUn_NW_015503630v1)
#    max 27160941 (chr3R) median 320
# %21.64 masked total, %21.71 masked real

    rm /gbdb/droSim2/droSim2.2bit
    ln -s `pwd`/droSim2.2bit /gbdb/droSim2/droSim2.2bit

#########################################################################
# CREATE MICROSAT TRACK (DONE - 2016-11-01 - Hiram)
    ssh hgwdev
    mkdir /cluster/data/droSim2/bed/microsat
    cd /cluster/data/droSim2/bed/microsat

    awk '($5==2 || $5==3) && $6 >= 15 && $8 == 100 && $9 == 0 {printf("%s\t%s\t%s\t%dx%s\n", $1, $2, $3, $6, $16);}' \
       ../simpleRepeat/simpleRepeat.bed > microsat.bed

    hgLoadBed droSim2 microsat microsat.bed
    # Read 24885 elements of size 4 from microsat.bed

##########################################################################
## WINDOWMASKER (DONE - 2016-11-01 - Hiram)

    mkdir /hive/data/genomes/droSim2/bed/windowMasker
    cd /hive/data/genomes/droSim2/bed/windowMasker
    time (doWindowMasker.pl -buildDir=`pwd` -workhorse=hgwdev \
        -dbHost=hgwdev droSim2) > do.log 2>&1
    #  real    5m1.607s

    # Masking statistics
    cat faSize.droSim2.cleanWMSdust.txt
# 124963774 bases (378345 N's 124585429 real 97623025 upper 26962404 lower)
#    in 7619 sequences in 1 files
# Total size: mean 16401.6 sd 603260.6 min 200 (chrUn_NW_015503630v1)
#    max 27160941 (chr3R) median 320
# %21.58 masked total, %21.64 masked real

    cat fb.droSim2.rmsk.windowmaskerSdust.txt
    #  6298577 bases of 124963774 (5.040%) in intersection

#########################################################################
# run up idKeys files for ncbiRefSeq (DONE - 2016-11-01 - Hiram)
    mkdir /hive/data/genomes/droSim2/bed/idKeys
    cd /hive/data/genomes/droSim2/bed/idKeys

    doIdKeys.pl -twoBit /hive/data/genomes/droSim2/droSim2.unmasked.2bit \
       -buildDir=`pwd` droSim2

    cat droSim2.keySignature.txt
    #   42f0f3041c6956e26676c502529a0331

##########################################################################
# ncbiRefSeq - (TBD - 2016-06-24 - Hiram)

##########################################################################
# cpgIslands - (DONE - 2016-11-01 - Hiram)
    mkdir /hive/data/genomes/droSim2/bed/cpgIslands
    cd /hive/data/genomes/droSim2/bed/cpgIslands
    time (doCpgIslands.pl -dbHost=hgwdev -bigClusterHub=ku \
      -workhorse=hgwdev -smallClusterHub=ku droSim2) > do.log 2>&1
    #   real    1m3.706s

    cat fb.droSim2.cpgIslandExt.txt
    # 13417596 bases of 124963774 (10.737%) in intersection

##############################################################################
# genscan - (DONE - 2016-11-01 - Hiram)
    mkdir /hive/data/genomes/droSim2/bed/genscan
    cd /hive/data/genomes/droSim2/bed/genscan
    time (doGenscan.pl -buildDir=`pwd` -workhorse=hgwdev -dbHost=hgwdev \
      -bigClusterHub=ku droSim2) > do.log 2>&1
    # real    20m37.096s

    cat fb.droSim2.genscan.txt
    # 17689863 bases of 124963774 (14.156%) in intersection

    cat fb.droSim2.genscanSubopt.txt
    # 605801 bases of 124963774 (0.485%) in intersection

########################################################################
# Create kluster run files (TBD - 2016-06-24 - Hiram)

    # numerator is droSim2 gapless bases "real" as reported by:
    featureBits -noRandom -noHap droSim2 gap
    # 0 bases of 3080431298 (0.000%) in intersection


    # denominator is hg19 gapless bases as reported by:
    #   featureBits -noRandom -noHap hg19 gap
    #     234344806 bases of 2861349177 (8.190%) in intersection
    # 1024 is threshold used for human -repMatch:
    calc \( 3080431298 / 2861349177 \) \* 1024
    #  ( 3080431298 / 2861349177 ) * 1024 = 1102.403605

    # ==> use -repMatch=1100 according to size scaled up from 1024 for human.
    #   and rounded down to nearest 50
    cd /hive/data/genomes/droSim2
    blat droSim2.2bit \
         /dev/null /dev/null -tileSize=11 -makeOoc=jkStuff/droSim2.11.ooc \
        -repMatch=1100
    #   Wrote 31384 overused 11-mers to jkStuff/droSim2.11.ooc

    # there are no non-bridged gaps (there no gaps at all)
    hgsql -e 'select count(*) from gap;' droSim2
# +----------+
# | count(*) |
# +----------+
# |        0 |
# +----------+

    hgsql -e 'select count(*) from gap where bridge="no";' droSim2
# +----------+
# | count(*) |
# +----------+
# |        0 |
# +----------+

    # if there were non-bridged gaps, make up a nonBridged.lft file

    #   check non-bridged gaps to see what the typical size is:
#    hgsql -N \
#         -e 'select * from gap where bridge="no" order by size;' droSim2 \
#         | sort -k7,7nr | ave -col=7 stdin
    #   most non-bridged gaps have size = 100
    #   decide on a minimum gap for this break, use either 100 or 5000 will
    #   generate 13387 liftOver rows, but if use 6000, only got 11703 rows.
    #   so use 100 here to get more liftOver row.
#     gapToLift -verbose=2 -minGap=100 droSim2 jkStuff/nonBridged.lft \
#         -bedFile=jkStuff/nonBridged.bed

########################################################################
# GENBANK AUTO UPDATE (TBD - 2016-07-22 - Hiram)
    ssh hgwdev
    cd $HOME/kent/src/hg/makeDb/genbank
    git pull
    # /cluster/data/genbank/data/organism.lst shows:
    # #organism     mrnaCnt estCnt  refSeqCnt
    # Gorilla gorilla 591     0       88
    # Gorilla gorilla gorilla 8       0       0

    # Edit src/lib/gbGenome.c to add new species

    # edit etc/genbank.conf to add droSim2 just after balAcu1

# Gorilla
droSim2.serverGenome = /hive/data/genomes/droSim2/droSim2.2bit
droSim2.clusterGenome = /hive/data/genomes/droSim2/droSim2.2bit
droSim2.ooc = /hive/data/genomes/droSim2/jkStuff/droSim2.11.ooc
droSim2.lift = no
droSim2.perChromTables = no
droSim2.refseq.mrna.native.pslCDnaFilter  = ${ordered.refseq.mrna.native.pslCDnaFilter}
droSim2.refseq.mrna.xeno.pslCDnaFilter    = ${ordered.refseq.mrna.xeno.pslCDnaFilter}
droSim2.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter}
droSim2.genbank.mrna.xeno.pslCDnaFilter   = ${ordered.genbank.mrna.xeno.pslCDnaFilter}
droSim2.genbank.est.native.pslCDnaFilter  = ${ordered.genbank.est.native.pslCDnaFilter}
droSim2.genbank.est.xeno.pslCDnaFilter    = ${ordered.genbank.est.xeno.pslCDnaFilter}
droSim2.downloadDir = droSim2
# default yes refseq.mrna.native refseq.mrna.xeno genbank.mrna.native
# default yes genbank.est.native
# default no genbank.mrna.xeno genbank.est.xeno

    git commit -m "Added droSim2 - Gorilla refs #17580" etc/genbank.conf
    git push
    # update /cluster/data/genbank/:
    make etc-update

    screen      #  control this business with a screen since it takes a while
    cd /cluster/data/genbank

    time ./bin/gbAlignStep -initial droSim2
    # real    67m3.917s

    # logFile: var/build/logs/2016.07.05-12:53:02.droSim2.initalign.log
    # tail -2 var/build/logs/2016.07.05-12:53:02.droSim2.initalign.log
# hgwdev 2016.07.05-13:59:57 droSim2.initalign: Succeeded: droSim2
# hgwdev 2016.07.05-14:00:06 droSim2.initalign: finish

    #   To re-do, rm the dir first:
    #     /cluster/data/genbank/work/initial.droSim2

    # load database when finished
    ssh hgwdev
    cd /cluster/data/genbank
    time ./bin/gbDbLoadStep -drop -initialLoad droSim2
    # real    18m33.387s
    tail -1 var/dbload/hgwdev/logs/2016.07.21-23:42:20.droSim2.dbload.log
# hgwdev 2016.07.22-00:00:53 droSim2.dbload: finish

    # enable daily alignment and update of hgwdev
    cd ~/kent/src/hg/makeDb/genbank
    git pull
    # add droSim2 to:
    #   etc/align.dbs etc/hgwdev.dbs
    git add etc/align.dbs etc/hgwdev.dbs
    git commit -m "Added droSim2 - Gorilla  - refs #17580" etc/align.dbs etc/hgwdev.dbs
    git push
    make etc-update

#############################################################################
# augustus gene track (DONE - 2016-11-01 - Hiram)

    mkdir /hive/data/genomes/droSim2/bed/augustus
    cd /hive/data/genomes/droSim2/bed/augustus
    time (doAugustus.pl -buildDir=`pwd` -bigClusterHub=ku \
        -species=fly -dbHost=hgwdev \
           -workhorse=hgwdev droSim2) > do.log 2>&1
    # real    79m54.233s

    cat fb.droSim2.augustusGene.txt
    # 22385355 bases of 124963774 (17.913%) in intersection

############################################################################
# construct liftOver to gorGor4 (TBD - 2016-06-24,26 - Hiram)
    screen -S gorGor4	# manage this longish running job in a screen
    mkdir /hive/data/genomes/droSim2/bed/blat.gorGor4.2016-06-24
    cd /hive/data/genomes/droSim2/bed/blat.gorGor4.2016-06-24
    # check it with -debug first to see if it is going to work:
    time doSameSpeciesLiftOver.pl -buildDir=`pwd` -bigClusterHub=ku \
	-ooc=/hive/data/genomes/droSim2/jkStuff/droSim2.11.ooc \
	-debug -dbHost=hgwdev -workhorse=hgwdev droSim2 gorGor4
    # real    0m2.154s

    # if that is OK, then run it:
    time (doSameSpeciesLiftOver.pl -buildDir=`pwd` -bigClusterHub=ku \
	-ooc=/hive/data/genomes/droSim2/jkStuff/droSim2.11.ooc \
	-dbHost=hgwdev -workhorse=hgwdev droSim2 gorGor4) > do.log 2>&1
    #	real    2412m36.913s

    # verify this file exists:
    #	/gbdb/droSim2/liftOver/droSim2ToGorGor4.over.chain.gz
    # and try out the conversion on genome-test from droSim2 to gorGor4

############################################################################
#  BLATSERVERS ENTRY (TBD - 2016-08-05 - Hiram)
#	After getting a blat server assigned by the Blat Server Gods,
    ssh hgwdev

    hgsql -e 'INSERT INTO blatServers (db, host, port, isTrans, canPcr) \
	VALUES ("droSim2", "blat1d", "17868", "1", "0"); \
	INSERT INTO blatServers (db, host, port, isTrans, canPcr) \
	VALUES ("droSim2", "blat1d", "17869", "0", "1");' \
	    hgcentraltest
    #	test it with some sequence

############################################################################
## default position (TBD - 2016-08-04 - Hiram)
    ssh hgwdev
    hgsql -e 'update dbDb set defaultPos="CYUI01015056v1:3670206-3687174"
	where name="droSim2";' hgcentraltest

#########################################################################
# all.joiner update, downloads and in pushQ - (TBD - 2016-08-08 - Hiram)
    cd $HOME/kent/src/hg/makeDb/schema
    # fixup all.joiner until this is a clean output
    joinerCheck -database=droSim2 -tableCoverage all.joiner
    joinerCheck -database=droSim2 -times all.joiner
    joinerCheck -database=droSim2 -keys all.joiner

    cd /hive/data/genomes/droSim2
    time (makeDownloads.pl droSim2) > downloads.log 2>&1
    #  real    19m52.657s

    #   now ready for pushQ entry
    mkdir /hive/data/genomes/droSim2/pushQ
    cd /hive/data/genomes/droSim2/pushQ
    time makePushQSql.pl droSim2 > droSim2.pushQ.sql 2> stderr.out
    #   real    11m56.179s

    #   check for errors in stderr.out, some are OK, e.g.:
    # WARNING: droSim2 does not have ucscToINSDC
    # WARNING: hgwdev does not have /gbdb/droSim2/wib/gc5Base.wib
    # WARNING: hgwdev does not have /gbdb/droSim2/wib/quality.wib
    # WARNING: hgwdev does not have /gbdb/droSim2/bbi/qualityBw/quality.bw
    # WARNING: droSim2 does not have seq
    # WARNING: droSim2 does not have extFile
    # WARNING: droSim2 does not have estOrientInfo

    #   copy it to hgwbeta
    scp -p droSim2.pushQ.sql qateam@hgwbeta:/tmp/
    ssh qateam@hgwbeta "./bin/x86_64/hgsql qapushq < /tmp/droSim2.pushQ.sql"

    #   in that pushQ entry walk through each entry and see if the
    #   sizes will set properly

###########################################################################
# LASTZ D. schellia droSec1 (DONE 2020-06-30 - Hiram)
    mkdir /hive/data/genomes/droSim2/bed/lastzDroSec1.2020-06-30
    cd /hive/data/genomes/droSim2/bed/lastzDroSec1.2020-06-30

    cat << '_EOF_' > DEF
    printf '# D. simulans vs. D. schellia
BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz
BLASTZ_H=2000
BLASTZ_Y=3400
BLASTZ_L=4000
BLASTZ_K=2200
BLASTZ_Q=/hive/data/staging/data/blastz/HoxD55.q

# TARGET - D. simulans
SEQ1_DIR=/hive/data/genomes/droSim2/droSim2.2bit
SEQ1_CHUNK=5000000
SEQ1_LAP=10000
SEQ1_LEN=/hive/data/genomes/droSim2/chrom.sizes

# QUERY - D. schellia
SEQ2_DIR=/hive/data/genomes/droSec1/droSec1.2bit
SEQ2_CHUNK=5000000
SEQ2_LAP=10000
SEQ2_LEN=/hive/data/genomes/droSec1/chrom.sizes

BASE=/hive/data/genomes/droSim2/bed/lastzDroSec1.2020-06-30
TMPDIR=/dev/shm
' > DEF

    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
        -chainMinScore=3000  -chainLinearGap=loose \
        -syntenicNet -fileServer=hgwdev \
    -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku) > do.log 2>&1
    # real    170m54.091s

    cat fb.droSim2.chainDroSec1Link.txt
    # 117906809 bases of 124963774 (94.353%) in intersection

    cat fb.droSim2.chainSynDroSec1Link.txt
    # 110785279 bases of 124963774 (88.654%) in intersection

    time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` droSim2 droSec1) > rbest.log 2>&1 &
    # real    3m47.266s

    cat fb.droSim2.chainRBest.DroSec1.txt
    # 113514069 bases of 124963774 (90.838%) in intersection

    #   running the swap
    mkdir /hive/data/genomes/droSec1/bed/blastz.droSim2.swap
    cd /hive/data/genomes/droSec1/bed/blastz.droSim2.swap
    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/droSim2/bed/lastzDroSec1.2020-06-30/DEF \
        -swap -chainMinScore=3000 -chainLinearGap=loose \
          -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1 &
    # real    6m22.506s

    cat fb.droSec1.chainDroSim2Link.txt
    # 134191023 bases of 157238575 (85.342%) in intersection
    cat fb.droSec1.chainSynDroSim2Link.txt
    # 112329362 bases of 157238575 (71.439%) in intersection

    time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` droSec1 droSim2) > rbest.log 2>&1 &
    # real    4m15.291s

    cat fb.droSec1.chainRBest.DroSim2.txt
    # 113366730 bases of 157238575 (72.099%) in intersection

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