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

# This file describes browser build for the felCat8
# cat/Felis catus -- International Cat Genome Sequencing Consortium
# This is the female Abyssinian cat named Cinnamon kept by
# Dr. Kristina Narfstrom at the University of Missouri

#############################################################################
# fetch sequence from new style download directory (DONE - 2014-11-20 - Hiram)
    # NCBI has redesigned their FTP download site, new type of address
    #      and naming scheme
    mkdir -p /hive/data/genomes/felCat8/genbank
    cd /hive/data/genomes/felCat8/genbank

    rsync -L -a -P \
rsync://ftp.ncbi.nlm.nih.gov/genomes/genbank/vertebrate_mammalian/Felis_catus/latest_assembly_versions/GCA_000181335.3_Felis_catus_8.0/ ./

    # measure what we have here:
    faSize \
GCA_000181335.3_Felis_catus_8.0_assembly_structure/Primary_Assembly/assembled_chromosomes/FASTA/*.fna.gz \
GCA_000181335.3_Felis_catus_8.0_assembly_structure/Primary_Assembly/unlocalized_scaffolds/FASTA/chr*.unlocalized.scaf.fna.gz \
GCA_000181335.3_Felis_catus_8.0_assembly_structure/Primary_Assembly/unplaced_scaffolds/FASTA/unplaced.scaf.fna.gz
    # 2641325249 bases (41642089 N's 2599683160 real 2599683160 upper 0 lower)
    #   in 267624 sequences in 39 files
    # Total size: mean 9869.5 sd 1168454.0 min 152 (AANG03201581.1)
    #    max 240380223 (CM001378.2) median 654
    # %0.00 masked total, %0.00 masked real

    # note that these totals do not include chrM since the GenBank ftp directory
    # did not include a non-nuclear directory

#############################################################################
# fixup to UCSC naming scheme (DONE - 2014-11-20 - Hiram)
    mkdir /hive/data/genomes/felCat8/ucsc
    cd /hive/data/genomes/felCat8/ucsc

    time ~/kent/src/hg/makeDb/doc/felCat8/ucscCompositeAgp.pl \
../genbank/GCA_000181335.3_Felis_catus_8.0_assembly_structure/Primary_Assembly

# CM001393.2 E3
# CM001383.2 B3
# CM001382.2 B2
#   CM001380.2 A3
# CM001386.2 C2
# CM001391.2 E1
# CM001390.2 D4
# CM001392.2 E2
# CM001385.2 C1
# CM001389.2 D3
# CM001388.2 D2
# CM001384.2 B4
# CM001395.2 F2
# CM001381.2 B1
# CM001394.2 F1
# CM001387.2 D1
# CM001378.2 A1
# CM001379.2 A2
# CM001396.2 X

# real    0m32.751s

    time ~/kent/src/hg/makeDb/doc/felCat8/unlocalized.pl \
../genbank/GCA_000181335.3_Felis_catus_8.0_assembly_structure/Primary_Assembly

# chrD2
# chrD3
# chrA1
# chrB4
# chrA2
# chrE1
# chrC1
# chrF2
# chrB2
# chrE3
# chrC2
# chrB1
# chrX
# chrD1
# chrD4
# chrA3
# chrB3
# chrE2
# chrF1

    # real    0m8.317s

    time ~/kent/src/hg/makeDb/doc/felCat8/unplaced.pl \
../genbank/GCA_000181335.3_Felis_catus_8.0_assembly_structure/Primary_Assembly
    # real    0m2.527s

    # verify nothing lost compared to genbank:
    faSize *.fa
    # 2641325249 bases (41642089 N's 2599683160 real 2599683160 upper 0 lower)
    #   in 267624 sequences in 39 files
    # Total size: mean 9869.5 sd 1168454.0 min 152 (chrUn_AANG03201581v1)
    #  max 240380223 (chrA1) median 654
    # %0.00 masked total, %0.00 masked real

    # same numbers as above.

#############################################################################
#  Initial database build (DONE - 2014-11-20 - Hiram)

    cd /hive/data/genomes/felCat8
    cat << '_EOF_' > felCat8.config.ra
# Config parameters for makeGenomeDb.pl:
db felCat8
clade mammal
genomeCladePriority 17
scientificName Felis catus
commonName Cat
assemblyDate Nov. 2014
assemblyLabel International Cat Genome Sequencing Consortium
assemblyShortLabel ICGSC Felis_catus_8.0
orderKey 2417
# chrM bioproject: 10762
mitoAcc NC_001700.1
fastaFiles /hive/data/genomes/felCat5/ucsc/*.fa
agpFiles /hive/data/genomes/felCat5/ucsc/*.agp
# qualFiles none
dbDbSpeciesDir cat
photoCreditURL http://www.genome.gov/pressDisplay.cfm?photoID=42
photoCreditName Dr. Kristina Narfstrom
ncbiGenomeId 78
ncbiAssemblyId 1373248
ncbiAssemblyName Felis_catus_8.0
ncbiBioProject 16726
genBankAccessionID GCA_000181335.3
taxId 9685
'_EOF_'
    # << happy emacs

    # verify sequence and AGP are OK:
    time makeGenomeDb.pl -workhorse=hgwdev -dbHost=hgwdev -fileServer=hgwdev \
         -stop=agp felCat8.config.ra > agp.log 2>&1
    # real    3m36.748s

    # then finish it off:
    time nice -n +19 makeGenomeDb.pl -workhorse=hgwdev -dbHost=hgwdev \
       -fileServer=hgwdev -continue=db felCat8.config.ra > db.log 2>&1
    # real    27m30.762s

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

#########################################################################
# add chromAlias table (DONE - 2017-12-14 - Hiram)

    mkdir /hive/data/genomes/felCat8/bed/chromAlias
    cd /hive/data/genomes/felCat8/bed/chromAlias

    hgsql -N -e 'select chrom,name from ucscToRefSeq;' felCat8 \
        > ucsc.refseq.tab
    hgsql -N -e 'select chrom,name from ucscToINSDC;' felCat8 \
        | grep -v chrM > ucsc.genbank.tab
    printf "chrM\tU20753.1\n" >> ucsc.genbank.tab

    join -t$'\t' ../idKeys/felCat8.idKeys.txt \
	../../ensembl/ensemblFelCat8.idKeys.txt \
	| cut -f2,3 | sort > ucsc.ensembl.tab

    ~/kent/src/hg/utils/automation/chromAlias.pl
    sort -o felCat8.chromAlias.tab felCat8.chromAlias.tab

for t in refseq genbank ensembl
do
  c0=`cat ucsc.$t.tab | wc -l`
  c1=`grep $t felCat8.chromAlias.tab | wc -l`
  ok="OK"
  if [ "$c0" -ne "$c1" ]; then
     ok="ERROR"
  fi
  printf "# checking $t: $c0 =? $c1 $ok\n"
done
# checking refseq: 267625 =? 267625 OK
# checking genbank: 267625 =? 267625 OK
# checking ensembl: 267625 =? 267625 OK

    hgLoadSqlTab felCat8 chromAlias ~/kent/src/hg/lib/chromAlias.sql \
        felCat8.chromAlias.tab

##########################################################################
# fixup search rule for assembly track/gold table (DONE - 2015-03-20 - Hiram)
    hgsql -N -e "select frag from gold;" felCat8 | sort | head -1
AANG03000001.1

    # there are other naming patterns:
    hgsql -N -e "select frag from gold;" felCat8 | sort | grep -v AANG | head -2
AC145332.48
AC233257.1

    hgsql -N -e "select frag from gold;" felCat8 | sort | tail -2
AY152836.1
NC_001700.1

    # verify this rule will find them all or eliminate them all:
    hgsql -N -e "select frag from gold;" felCat8 | wc -l
    # 367856

    hgsql -N -e "select frag from gold;" felCat8 \
       | egrep -e '[AN][ACY][N0-9_][G0-9][0-9]+(\.[0-9]+)?' | wc -l
    # 367856

    hgsql -N -e "select frag from gold;" felCat8 \
       | egrep -v -e '[AN][ACY][N0-9_][G0-9][0-9]+(\.[0-9]+)?' | wc -l
    # 0

    # hence, add to trackDb/cat/felCat8/trackDb.ra
searchTable gold
shortCircuit 1
termRegex [AN][ACY][N0-9_][G0-9][0-9]+(\.[0-9]+)?
query select chrom,chromStart,chromEnd,frag from %s where frag like '%s%%'
searchPriority 8

##########################################################################
# running repeat masker (DONE - 2014-11-21 - Hiram)
    mkdir /hive/data/genomes/felCat8/bed/repeatMasker
    cd /hive/data/genomes/felCat8/bed/repeatMasker
    time  doRepeatMasker.pl -buildDir=`pwd` \
        -bigClusterHub=ku -dbHost=hgwdev -workhorse=hgwdev \
        -smallClusterHub=ku felCat8 > do.log 2>&1
    # real    453m35.159s

    cat faSize.rmsk.txt
    # 2641342258 bases (41642089 N's 2599700169 real 1446287702 upper
    # 1153412467 lower) in 267625 sequences in 1 files
    # Total size: mean 9869.6 sd 1168451.9 min 152 (chrUn_AANG03201581v1)
    #    max 240380223 (chrA1) median 654
    # %43.67 masked total, %44.37 masked real

    egrep -i "versi|relea" do.log
    # RepeatMasker version open-4.0.5
    #    January 31 2015 (open-4-0-5) version of RepeatMasker
    # CC   RELEASE 20140131;

    time featureBits -countGaps felCat8 rmsk
    # 1154358179 bases of 2641342258 (43.703%) in intersection
    # real    2m13.123s

    # 1289639153 bases of 2670044500 (48.300%) in intersection
    # why is it different than the faSize above ?
    # because rmsk masks out some N's as well as bases, the count above
    #   separates out the N's from the bases, it doesn't show lower case N's

##########################################################################
# running simple repeat (DONE 2014-11-21 - Hiram)

    mkdir /hive/data/genomes/felCat8/bed/simpleRepeat
    cd /hive/data/genomes/felCat8/bed/simpleRepeat
    time doSimpleRepeat.pl -buildDir=`pwd` -bigClusterHub=ku \
        -dbHost=hgwdev -workhorse=hgwdev -smallClusterHub=ku \
        felCat8 > do.log 2>&1
    # real    140m2.826s

    cat fb.simpleRepeat
    # 54549425 bases of 2599716822 (2.098%) in intersection

    # add to rmsk after it is done:
    cd /hive/data/genomes/felCat8
    twoBitMask felCat8.rmsk.2bit \
        -add bed/simpleRepeat/trfMask.bed felCat8.2bit
    #   you can safely ignore the warning about fields >= 13
    twoBitToFa felCat8.2bit stdout | faSize stdin > faSize.felCat8.2bit.txt
    cat faSize.felCat8.2bit.txt
    # 2641342258 bases (41642089 N's 2599700169 real 1445054690 upper
    # 1154645479 lower) in 267625 sequences in 1 files
    # Total size: mean 9869.6 sd 1168451.9 min 152 (chrUn_AANG03201581v1)
    #    max 240380223 (chrA1) median 654
    # %43.71 masked total, %44.41 masked real

    rm /gbdb/felCat8/felCat8.2bit
    ln -s `pwd`/felCat8.2bit /gbdb/felCat8/felCat8.2bit

##########################################################################
# CREATE MICROSAT TRACK (DONE - 2015-06-22 - Hiram)
     ssh hgwdev
     mkdir /cluster/data/felCat8/bed/microsat
     cd /cluster/data/felCat8/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 felCat8 microsat microsat.bed
    #	Read 126733 elements of size 4 from microsat.bed

##########################################################################
## WINDOWMASKER (DONE - 2014-11-21 - Hiram)

    mkdir /hive/data/genomes/felCat8/bed/windowMasker
    cd /hive/data/genomes/felCat8/bed/windowMasker
    time nice -n +19 doWindowMasker.pl -buildDir=`pwd` -workhorse=hgwdev \
        -dbHost=hgwdev felCat8 > do.log 2>&1
    # real    613m12.862s

    # Masking statistics
    cat faSize.felCat8.cleanWMSdust.txt
    # 2641342258 bases (41642089 N's 2599700169 real 1691420529 upper
    # 908279640 lower) in 267625 sequences in 1 files
    # Total size: mean 9869.6 sd 1168451.9 min 152 (chrUn_AANG03201581v1)
    #   max 240380223 (chrA1) median 654
    # %34.39 masked total, %34.94 masked real

    cat fb.felCat8.rmsk.windowmaskerSdust.txt
    # 649247774 bases of 2641342258 (24.580%) in intersection

##########################################################################
# cpgIslands - (DONE - 2014-11-25 - Hiram)
    mkdir /hive/data/genomes/felCat8/bed/cpgIslands
    cd /hive/data/genomes/felCat8/bed/cpgIslands
    time doCpgIslands.pl -dbHost=hgwdev -bigClusterHub=ku \
      -workhorse=hgwdev -smallClusterHub=ku felCat8 > do.log 2>&1
    # real    1589m30.221s

    cat fb.felCat8.cpgIslandExt.txt
    # 44372623 bases of 2599716822 (1.707%) in intersection

##############################################################################
# cpgIslands on UNMASKED sequence (DONE - 2014-11-25 - Hiram)
    mkdir /hive/data/genomes/felCat8/bed/cpgIslandsUnmasked
    cd /hive/data/genomes/felCat8/bed/cpgIslandsUnmasked

    # run stepwise so the loading can be done in a different table
    time doCpgIslands.pl -dbHost=hgwdev -bigClusterHub=ku -buildDir=`pwd` \
       -tableName=cpgIslandExtUnmasked \
          -maskedSeq=/hive/data/genomes/felCat8/felCat8.unmasked.2bit \
             -workhorse=hgwdev -smallClusterHub=ku felCat8 > do.log 2>&1
    # real    1585m9.656s

    cat fb.felCat8.cpgIslandExtUnmasked.txt
    # 69023548 bases of 2599716822 (2.655%) in intersection

#############################################################################
# cytoBandIdeo - (DONE - 2015-12-02 - Hiram)
    mkdir /hive/data/genomes/felCat8/bed/cytoBand
    cd /hive/data/genomes/felCat8/bed/cytoBand
    makeCytoBandIdeo.csh felCat8

#########################################################################
# genscan - (DONE - 2014-11-25,12-02 - Hiram)
    mkdir /hive/data/genomes/felCat8/bed/genscan
    cd /hive/data/genomes/felCat8/bed/genscan
    time doGenscan.pl -buildDir=`pwd` -workhorse=hgwdev -dbHost=hgwdev \
      -bigClusterHub=ku felCat8 > do.log 2>&1
    # real    2252m4.489s
    # two jobs failed, running with reduced window size 2,000,000
# ./runGsBigLastTwo.csh chrC1 021 gtf/021/chrC1.gtf pep/021/chrC1.pep subopt/021/chrC1.bed &
# ./runGsBigLastTwo.csh chrD1 028 gtf/028/chrD1.gtf pep/028/chrD1.pep subopt/028/chrD1.bed
# wait

    # continuing
    time doGenscan.pl -continue=makeBed  -buildDir=`pwd` -workhorse=hgwdev \
      -dbHost=hgwdev -bigClusterHub=ku felCat8 > makeBed.log 2>&1
    # real    14m46.164s

    cat fb.felCat8.genscan.txt
    # 60883009 bases of 2599716822 (2.342%) in intersection

    cat fb.felCat8.genscanSubopt.txt
    # 52372380 bases of 2599716822 (2.015%) in intersection

########################################################################
# Create kluster run files (DONE - 2014-12-02 - Hiram)

    # numerator is felCat8 gapless bases "real" as reported by:
    featureBits -noRandom -noHap felCat8 gap
    # 36037214 bases of 2383192705 (1.512%) 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 \( 2383192705 / 2861349177 \) \* 1024
    #  ( 2383192705 / 2861349177 ) * 1024 = 852.880644

    # ==> use -repMatch=800 according to size scaled down from 1024 for human.
    #   and rounded down to nearest 50
    cd /hive/data/genomes/felCat8
    time blat felCat8.2bit \
         /dev/null /dev/null -tileSize=11 -makeOoc=jkStuff/felCat8.11.ooc \
        -repMatch=800
    #  Wrote 36446 overused 11-mers to jkStuff/felCat8.11.ooc
    #  real    1m20.620s

    #   check non-bridged gaps to see what the typical size is:
    hgsql -N -e 'select * from gap where bridge="no" order by size;' \
       felCat8 | ave -col=7 stdin
# Q1 100.000000
# median 100.000000
# Q3 100.000000
# average 100.000000
# min 100.000000
# max 100.000000
# count 303
# total 30300.000000
# standard deviation 0.000000

    # they are all 100 bases
    gapToLift -verbose=2 -minGap=100 felCat8 jkStuff/felCat8.nonBridged.lft \
        -bedFile=jkStuff/felCat8.nonBridged.bed

    cat jkStuff/felCat8.nonBridged.bed | awk '{printf "%s\t%d\n", $4,$3-$2}' \
        | sort -k2nr > jkStuff/nonBridged.sizes
    n50.pl jkStuff/nonBridged.sizes
#       reading: nonBridged.sizes
#       contig count: 267928, total size: 2641311958, one half size:
#       1320655979
# cumulative    N50 count       contig  contig size
1307787463      44      chrC1.08        18169384
1320655979 one half size
1325860434      45      chrX.28 18072971

########################################################################
# GENBANK AUTO UPDATE (WORKING - 2014-12-02,05 - Hiram)
    ssh hgwdev
    cd $HOME/kent/src/hg/makeDb/genbank
    git pull
    # /cluster/data/genbank/data/organism.lst shows:
    # #organism       mrnaCnt estCnt  refSeqCnt
    # Felis catus     2392    923     399

    # edit etc/genbank.conf to add felCat8 just before felCat5
# Nov. 2014 International Cat Genome Sequencing Consortium Felis_catus_8.0
# felCat8 (Cat)
felCat8.serverGenome = /hive/data/genomes/felCat8/felCat8.2bit
felCat8.clusterGenome = /hive/data/genomes/felCat8/felCat8.2bit
felCat8.ooc = /hive/data/genomes/felCat8/jkStuff/felCat8.11.ooc
felCat8.lift = /hive/data/genomes/felCat8/jkStuff/felCat8.nonBridged.lift
felCat8.perChromTables = no
felCat8.refseq.mrna.native.pslCDnaFilter  = ${finished.refseq.mrna.native.pslCDnaFilter}
felCat8.refseq.mrna.xeno.pslCDnaFilter    = ${finished.refseq.mrna.xeno.pslCDnaFilter}
felCat8.genbank.mrna.native.pslCDnaFilter = ${finished.genbank.mrna.native.pslCDnaFilter}
felCat8.genbank.mrna.xeno.pslCDnaFilter   = ${finished.genbank.mrna.xeno.pslCDnaFilter}
felCat8.genbank.est.native.pslCDnaFilter  = ${finished.genbank.est.native.pslCDnaFilter}
felCat8.genbank.est.xeno.pslCDnaFilter    = ${finished.genbank.est.xeno.pslCDnaFilter}
felCat8.genbank.mrna.xeno.load  = yes
felCat8.downloadDir = felCat8
felCat8.refseq.mrna.native.load  = yes
felCat8.refseq.mrna.xeno.load = yes
felCat8.refseq.mrna.xeno.loadDesc  = yes
# felCat8.upstreamGeneTbl = refGene
# felCat8.upstreamMaf = multiz6way
# /hive/data/genomes/felCat8/bed/multiz6way/species.list

    git commit -m "Added felCat8; refs #14412" etc/genbank.conf
    git push
    # update /cluster/data/genbank/:
    make etc-update

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

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

    time ./bin/gbAlignStep -initial felCat8
    # logFile: var/build/logs/2014.12.02-11:51:04.felCat8.initalign.log
    #   real    1310m38.973s
    #   If necessary to restart from beginning, rm the dir first:
    #     /cluster/data/genbank/work/initial.felCat8

    # load database when finished
    ssh hgwdev
    cd /cluster/data/genbank
    time ./bin/gbDbLoadStep -drop -initialLoad felCat8
    # logFile: var/dbload/hgwdev/logs/2014.12.03-21:03:57.felCat8.dbload.log
    # real    82m44.925s

    # enable daily alignment and update of hgwdev
    cd ~/kent/src/hg/makeDb/genbank
    git pull
    # add felCat8 to:
    #   vi etc/align.dbs etc/hgwdev.dbs
    git commit -m "Added felCat8 - cat refs #14412" etc/align.dbs etc/hgwdev.dbs
    git push
    make etc-update

############################################################################
# construct liftOver to felCat5 (DONE - 2014-12-02 - Hiram)
    screen -S felCat5	# manage this longish running job in a screen
    mkdir /hive/data/genomes/felCat8/bed/blat.felCat5.2014-12-02
    cd /hive/data/genomes/felCat8/bed/blat.felCat5.2014-12-02
    # check it with -debug first to see if it is going to work:
    time doSameSpeciesLiftOver.pl -buildDir=`pwd` -bigClusterHub=ku \
	-ooc=/hive/data/genomes/felCat8/jkStuff/felCat8.11.ooc \
	-debug -dbHost=hgwdev -workhorse=hgwdev felCat8 felCat5
    #   real    0m1.838s
    # if that is OK, then run it:
    time (doSameSpeciesLiftOver.pl -buildDir=`pwd` -bigClusterHub=ku \
	-ooc=/hive/data/genomes/felCat8/jkStuff/felCat8.11.ooc \
	-dbHost=hgwdev -workhorse=hgwdev felCat8 felCat5) > do.log 2>&1
    #	real    454m20.649s

    # verify this file exists:
    #	/gbdb/felCat8/liftOver/felCat8ToFelCat5.over.chain.gz
    # and try out the conversion on genome-test from felCat8 to felCat5

#########################################################################
# ucscToINSDC table/track (DONE - 2014-12-09 - Hiram)

    mkdir /hive/data/genomes/felCat8/bed/ucscToINSDC
    cd /hive/data/genomes/felCat8/bed/ucscToINSDC
    # check for chrM in assembly:
    grep chrM ../../felCat8.agp
# chrM    1       17009   6       F       NC_001700.1     1       17009   +

    # use the accession name from there in this command (blank if none)
    ~/kent/src/hg/makeDb/doc/felCat8/ucscToINSDC.sh \
        ../../genbank/GCA_*assembly_structure/Primary_Assembly NC_001700.1

    awk '{printf "%s\t0\t%d\n", $1,$2}' ../../chrom.sizes \
         | sort > name.coordinate.tab
    join name.coordinate.tab ucscToINSDC.txt | tr '[ ]' '[\t]' \
         > ucscToINSDC.bed
    # should all be the same line count:
    wc -l *
    # 267625 name.coordinate.tab
    # 267625 ucscToINSDC.bed
    # 267625 ucscToINSDC.txt

    cut -f1 ucscToINSDC.bed | awk '{print length($0)}' | sort -n | tail -1
    # 27
    # use the 27 in this sed
    sed -e "s/21/27/" $HOME/kent/src/hg/lib/ucscToINSDC.sql \
         | hgLoadSqlTab felCat8 ucscToINSDC stdin ucscToINSDC.bed
    checkTableCoords felCat8
    # should cover %100 entirely:
    featureBits -countGaps felCat8 ucscToINSDC
    # 2641342258 bases of 2641342258 (100.000%) in intersection

############################################################################
#  BLATSERVERS ENTRY (DONE - 2015-03-20 - Hiram)
#	After getting a blat server assigned by the Blat Server Gods,
     ssh hgwdev

     # verify doesn't exist yet:
     hgsql -e 'select * from blatServers;' hgcentraltest | grep -i felcat
     # only shows felCat4 and felCat5

     hgsql -e 'INSERT INTO blatServers (db, host, port, isTrans, canPcr) \
	VALUES ("felCat8", "blat4d", "17856", "1", "0"); \
	INSERT INTO blatServers (db, host, port, isTrans, canPcr) \
	VALUES ("felCat8", "blat4d", "17857", "0", "1");' \
		hgcentraltest

     # verify entry:
     hgsql -e 'select * from blatServers;' hgcentraltest | grep -i felcat
     #    felCat8 blat4d  17856   1       0
     #    felCat8 blat4d  17857   0       1

     #	test it with some sequence

#########################################################################
# set default position (DONE - 2014-12-09 - Hiram)

    # equivalent to felCat5 position obtained by liftOver test in
    # the browser from felCat5 default position (RHO gene)
    hgsql -e \
'update dbDb set defaultPos="chrA2:54097485-54103554" where name="felCat8";' \
	hgcentraltest

#########################################################################
# all.joiner update, downloads and in pushQ - (DONE 2015-01-27 - Hiram)
    cd $HOME/kent/src/hg/makeDb/schema
    # fixup all.joiner until this is a clean output
    joinerCheck -database=felCat8 -keys all.joiner
    joinerCheck -database=felCat8 -tableCoverage all.joiner
    joinerCheck -database=felCat8 -times all.joiner

    cd /hive/data/genomes/felCat8
    time makeDownloads.pl felCat8 > downloads.log 2>&1
    #  real    23m40.246s

    #   now ready for pushQ entry
    mkdir /hive/data/genomes/felCat8/pushQ
    cd /hive/data/genomes/felCat8/pushQ
    # do not want transMap in the output:
    makePushQSql.pl felCat8 2> stderr.out | grep -v transMap > felCat8.pushQ.sql
    #   check for errors in stderr.out, some are OK, e.g.:
    # WARNING: hgwdev does not have /gbdb/felCat8/wib/gc5Base.wib
    # WARNING: hgwdev does not have /gbdb/felCat8/wib/quality.wib
    # WARNING: hgwdev does not have /gbdb/felCat8/bbi/quality.bw
    # WARNING: felCat8 does not have seq
    # WARNING: felCat8 does not have extFile

    #   copy it to hgwbeta
    scp -p felCat8.pushQ.sql qateam@hgwbeta:/tmp
    ssh qateam@hgwbeta './bin/x86_64/hgsql qapushq < /tmp/felCat8.pushQ.sql'
    #   in that pushQ entry walk through each entry and see if the
    #   sizes will set properly

#########################################################################
# LIFTOVER TO felCat9 (DONE - 2018-02-28 - Hiram)
    ssh hgwdev
    mkdir /hive/data/genomes/felCat8/bed/blat.felCat9.2018-02-28
    cd /hive/data/genomes/felCat8/bed/blat.felCat9.2018-02-28
    time (doSameSpeciesLiftOver.pl -verbose=2 -buildDir=`pwd` \
	-ooc=/hive/data/genomes/felCat8/jkStuff/felCat8.11.ooc \
        -bigClusterHub=ku -dbHost=hgwdev -workhorse=hgwdev \
         felCat8 felCat9) > do.log 2>&1 &
    # real    1047m54.841s

    # verify the convert link on the test browser is now active from felCat8 to
    # felCat9

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