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

# This file describes browser build for the ornAna2
# Platypus - Ornithorhynchus anatinus
## "Glennie"

# Assembly Name:  ASM227v2
# Organism name:  Ornithorhynchus anatinus
# Taxid:          9258
# Submitter:      Washington University (WashU)
# Date:           2007-2-14
# BioSample:      SAMN02953646
# Assembly type:  haploid
# Release type:   major
# Assembly level: Chromosome
# Genome representation: full
# GenBank Assembly Accession: GCA_000002275.2 (latest)
#
## Assembly-Units:
## GenBank Unit Accession       RefSeq Unit Accession   Assembly-Unit name
## GCA_000000135.2              Primary Assembly

## chrMt is NC_000891.1 -> http://www.ncbi.nlm.nih.gov/bioproject/10802

## http://www.ncbi.nlm.nih.gov/bioproject/PRJNA19039


#############################################################################
# fetch sequence from new style download directory (DONE - 2015-03-04 - Hiram)
    mkdir -p /hive/data/genomes/ornAna2/genbank
    cd /hive/data/genomes/ornAna2/genbank

    time rsync -L -a -P \
rsync://ftp.ncbi.nlm.nih.gov/genomes/genbank/vertebrate_mammalian/Ornithorhynchus_anatinus/all_assembly_versions/GCA_000002275.2_ASM227v2/ ./

    # sent 1102 bytes  received 1436188553 bytes  11353277.91 bytes/sec
    # total size is 1436008781  speedup is 1.00
    # real    2m6.484s

    # measure what we have here:
    faSize GCA_000002275.2_ASM227v2_genomic.fna.gz
    # 1996809494 bases (154575690 N's 1842233804 real 997282221
    #    upper 844951583 lower) in 201524 sequences in 1 files
    # Total size: mean 9908.5 sd 331991.7 min 108 (AAPN01446708.1)
    #    max 59581953 (CM000411.1) median 1069
    # %42.32 masked total, %45.87 masked real


#############################################################################
# fixup to UCSC naming scheme (DONE - 2015-03-09 - Hiram)
    mkdir /hive/data/genomes/ornAna2/ucsc
    cd /hive/data/genomes/ornAna2/ucsc

    time ~/kent/src/hg/makeDb/doc/ornAna2/ucscCompositeAgp.pl \
       ../genbank/GCA_000002275.2_ASM227v2_assembly_structure/Primary_Assembly
    # real    0m10.549s
    time ~/kent/src/hg/makeDb/doc/ornAna2/unplaced.pl \
       ../genbank/GCA_000002275.2_ASM227v2_assembly_structure/Primary_Assembly
    # real    0m26.479s
    time ~/kent/src/hg/makeDb/doc/ornAna2/unlocalized.pl \
       ../genbank/GCA_000002275.2_ASM227v2_assembly_structure/Primary_Assembly

    # verify nothing lost:
    faSize chr*.fa
    # 1996809494 bases (154575690 N's 1842233804 real 1842233804 upper
    #    0 lower) in 201524 sequences in 21 files
    # Total size: mean 9908.5 sd 331991.7 min 108 (chrUn_AAPN01446708v1)
    #    max 59581953 (chr3) median 1069
    # %0.00 masked total, %0.00 masked real

    # verify the fa and AGP files are compatible:
    faToTwoBit chr*.fa test.2bit
    cat chr*.agp | checkAgpAndFa stdin test.2bit 2>&1 | tail
    # All AGP and FASTA entries agree - both files are valid
    rm -f test.2bit

#############################################################################
#  Initial database build (DONE - 2015-03-09 - Hiram)

    cd /hive/data/genomes/ornAna2
    cat << '_EOF_' > ornAna2.config.ra
# Config parameters for makeGenomeDb.pl:
db ornAna2
clade mammal
genomeCladePriority 65
commonName Platypus
scientificName Ornithorhynchus anatinus
assemblyDate Feb. 2007
assemblyLabel WUGSC ASM227v2
assemblyShortLabel ASM227v2
orderKey 16409
# chrMt: http://www.ncbi.nlm.nih.gov/bioproject/10802
mitoAcc NC_000891.1
fastaFiles /cluster/data/ornAna2/ucsc/chr*.fa
agpFiles /cluster/data/ornAna2/ucsc/chr*.agp
dbDbSpeciesDir platypus
photoCreditURL http://commons.wikimedia.org/wiki/File:Platypus.jpg
photoCreditName Stefan Kraft - Wikimedia Commons
ncbiGenomeId 110
ncbiAssemblyId 237598
ncbiAssemblyName ASM227v2
ncbiBioProject 19039
genBankAccessionID GCA_000002275.2
taxId 9258
'_EOF_'
    # << happy emacs

    # verify sequence and AGP are OK:
    # temporary set sciName to just 'Bison bison' to get through the chrM
    #  identification
    time (makeGenomeDb.pl -workhorse=kolossus -dbHost=hgwdev \
       -fileServer=hgwdev -stop=agp ornAna2.config.ra) > agp.log 2>&1
    # *** All done!  (through the 'agp' step)
    # real    9m59.789s

    # then finish it off:
    time (makeGenomeDb.pl -workhorse=hgwdev -dbHost=hgwdev \
       -fileServer=hgwdev -continue=db ornAna2.config.ra) > db.log 2>&1
    # real    21m53.472s

    # check in the trackDb files created and add to trackDb/makefile
    # and clean up:
    rm -fr TemporaryTrackDbCheckout/

##########################################################################
# running repeat masker (DONE - 2015-03-10 - Hiram)
    mkdir /hive/data/genomes/ornAna2/bed/repeatMasker
    cd /hive/data/genomes/ornAna2/bed/repeatMasker
    time (doRepeatMasker.pl -buildDir=`pwd` \
        -bigClusterHub=ku -dbHost=hgwdev -workhorse=hgwdev \
        -smallClusterHub=ku ornAna2) > do.log 2>&1
    # real    253m47.814s

    # three identifiers failed, clean the result:
    mv ornAna2.sorted.fa.out ornAna2.sorted.fa.out.badIds
egrep -v \
  "chr1      28133788|chrUn_DS181657v1  719030|chrUn_DS213462v1     703" \
   ornAna2.sorted.fa.out.badIds > ornAna2.sorted.fa.out

    /cluster/bin/scripts/extractNestedRepeats.pl ornAna2.fa.out \
       | sort -k1,1 -k2,2n > ornAna2.nestedRepeats.bed

    # continuing:
    time (doRepeatMasker.pl -buildDir=`pwd` \
        -bigClusterHub=ku -dbHost=hgwdev -workhorse=hgwdev \
        -continue=mask -smallClusterHub=ku ornAna2) > mask.log 2>&1
    # real    19m51.592s

    cat faSize.rmsk.txt
    # 1996826513 bases (154575690 N's 1842250823 real 948454705 upper
    #    893796118 lower) in 201525 sequences in 1 files
    # Total size: mean 9908.6 sd 331990.9 min 108 (chrUn_AAPN01446708v1)
    #    max 59581953 (chr3) median 1069
    # %44.76 masked total, %48.52 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 ornAna2 rmsk
    # 894749490 bases of 1996826513 (44.809%) in intersection
    #   real    2m21.794s

    # 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 - 2015-03-10 - Hiram)

    mkdir /hive/data/genomes/ornAna2/bed/simpleRepeat
    cd /hive/data/genomes/ornAna2/bed/simpleRepeat
    time (doSimpleRepeat.pl -buildDir=`pwd` -bigClusterHub=ku \
        -dbHost=hgwdev -workhorse=hgwdev -smallClusterHub=ku \
        ornAna2) > do.log 2>&1
    # real    95m30.651s

    cat fb.simpleRepeat
    # 52678700 bases of 1842252119 (2.859%) in intersection

    # using the Window Masker result:
    cd /hive/data/genomes/ornAna2
    twoBitMask bed/repeatMasker/ornAna2.rmsk.2bit \
      -add bed/simpleRepeat/trfMask.bed  ornAna2.2bit
    #   you can safely ignore the warning about fields >= 13
    twoBitToFa ornAna2.2bit stdout | faSize stdin > faSize.ornAna2.2bit.txt
    cat faSize.ornAna2.2bit.txt
    # 1996826513 bases (154575690 N's 1842250823 real 947687014 upper
    #    894563809 lower) in 201525 sequences in 1 files
    # Total size: mean 9908.6 sd 331990.9 min 108 (chrUn_AAPN01446708v1)
    #    max 59581953 (chr3) median 1069
    # %44.80 masked total, %48.56 masked real

    rm /gbdb/ornAna2/ornAna2.2bit
    ln -s `pwd`/ornAna2.2bit /gbdb/ornAna2/ornAna2.2bit

##########################################################################
# CREATE MICROSAT TRACK (DONE - 2015-06-22 - Hiram)
     ssh hgwdev
     mkdir /cluster/data/ornAna2/bed/microsat
     cd /cluster/data/ornAna2/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 ornAna2 microsat microsat.bed
    #	Loaded 13365 elements of size 4

##########################################################################
## WINDOWMASKER (DONE - 2015-03-10 - Hiram)

    mkdir /hive/data/genomes/ornAna2/bed/windowMasker
    cd /hive/data/genomes/ornAna2/bed/windowMasker
    time (doWindowMasker.pl -buildDir=`pwd` -workhorse=hgwdev \
        -dbHost=hgwdev ornAna2) > do.log 2>&1
    # real    606m53.374s

    # Masking statistics
    cat faSize.ornAna2.cleanWMSdust.txt
    # 1996826513 bases (154575690 N's 1842250823 real 985358741 upper
    #    856892082 lower) in 201525 sequences in 1 files
    # Total size: mean 9908.6 sd 331990.9 min 108 (chrUn_AAPN01446708v1)
    #    max 59581953 (chr3) median 1069
    # %42.91 masked total, %46.51 masked real

    cat fb.ornAna2.rmsk.windowmaskerSdust.txt
    # 715265328 bases of 1996826513 (35.820%) in intersection

##########################################################################
# cpgIslands - (DONE - 2015-03-31 - Hiram)
    mkdir /hive/data/genomes/ornAna2/bed/cpgIslands
    cd /hive/data/genomes/ornAna2/bed/cpgIslands
    time (doCpgIslands.pl -dbHost=hgwdev -bigClusterHub=ku \
      -workhorse=hgwdev -smallClusterHub=ku ornAna2) > do.log 2>&1 &
    # real    75m14.279s

    cat fb.ornAna2.cpgIslandExt.txt
    # 43180726 bases of 1842252119 (2.344%) in intersection

##############################################################################
# cpgIslands on UNMASKED sequence (DONE - 2015-03-10 - Hiram)
    mkdir /hive/data/genomes/ornAna2/bed/cpgIslandsUnmasked
    cd /hive/data/genomes/ornAna2/bed/cpgIslandsUnmasked

    time (doCpgIslands.pl -dbHost=hgwdev -bigClusterHub=ku -buildDir=`pwd` \
       -tableName=cpgIslandExtUnmasked \
          -maskedSeq=/hive/data/genomes/ornAna2/ornAna2.unmasked.2bit \
             -workhorse=hgwdev -smallClusterHub=ku ornAna2) > do.log 2>&1
    # real    124m18.319s

    cat fb.ornAna2.cpgIslandExtUnmasked.txt
    # 101211831 bases of 1842252119 (5.494%) in intersection

#############################################################################
# cytoBandIdeo - (DONE - 2015-03-10 - Hiram)
    mkdir /hive/data/genomes/ornAna2/bed/cytoBand
    cd /hive/data/genomes/ornAna2/bed/cytoBand
    makeCytoBandIdeo.csh ornAna2

#########################################################################
# augustus - (DONE - 2015-06-19 - Hiram)
    mkdir /hive/data/genomes/ornAna2/bed/augustus
    cd /hive/data/genomes/ornAna2/bed/augustus
    time (doAugustus.pl -buildDir=`pwd` -bigClusterHub=ku \
    -species=chicken -dbHost=hgwdev -workhorse=hgwdev ornAna2) > do.log 2>&1
    # real    80m33.289s

    cat fb.ornAna2.augustusGene.txt
    # 27859792 bases of 1842252119 (1.512%) in intersection

#########################################################################
# genscan - (DONE - 2015-03-31 - Hiram)
    mkdir /hive/data/genomes/ornAna2/bed/genscan
    cd /hive/data/genomes/ornAna2/bed/genscan
    time (doGenscan.pl -buildDir=`pwd` -workhorse=hgwdev -dbHost=hgwdev \
      -bigClusterHub=ku ornAna2) > do.log 2>&1
    # real    110m50.427s

    cat fb.ornAna2.genscan.txt
    #   44600621 bases of 1842252119 (2.421%) in intersection

    cat fb.ornAna2.genscanSubopt.txt
    #   42596907 bases of 1842252119 (2.312%) in intersection

#########################################################################
# ucscToINSDC table/track (DONE - 2015-03-10 - Hiram)
    mkdir /hive/data/genomes/ornAna2/bed/ucscToINSDC
    cd /hive/data/genomes/ornAna2/bed/ucscToINSDC

    ~/kent/src/hg/utils/automation/ucscToINSDC.sh \
         ../../genbank/GCA_*assembly_structure/Primary_Assembly NC_000891.1

    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
    # verify all names are coming through, should be same line count:
    wc -l *
    #  201525 name.coordinate.tab
    #  201525 ucscToINSDC.bed
    #  201525 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 ornAna2 ucscToINSDC stdin ucscToINSDC.bed
    checkTableCoords ornAna2
    # should cover %100 entirely:
    featureBits -countGaps ornAna2 ucscToINSDC
    # 1996826513 bases of 1996826513 (100.000%) in intersection

#########################################################################
# fixup search rule for assembly track/gold table (DONE - 2015-03-10 - Hiram)
    hgsql -N -e "select frag from gold;" ornAna2 | sort | head -1
AAPN01000001.1

    hgsql -N -e "select frag from gold;" ornAna2 | sort | tail -2
AAPN01447149.1
NC_000891.1

    # verify this rule will find them all or eliminate them all:
    hgsql -N -e "select frag from gold;" ornAna2 | wc -l
    # 445349

    hgsql -N -e "select frag from gold;" ornAna2 \
       | egrep -e '[AN][AC][P_][N0]0[0-9]+(\.1)?' | wc -l
    # 445349

    hgsql -N -e "select frag from gold;" ornAna2 \
       | egrep -v -e '[AN][AC][P_][N0]0[0-9]+(\.1)?' | wc -l
    # 0

    # hence, add to trackDb/tarsier/ornAna2/trackDb.ra
searchTable gold
shortCircuit 1
termRegex [AN][AC][P_][N0]0[0-9]+(\.1)?
query select chrom,chromStart,chromEnd,frag from %s where frag like '%s%%'
searchPriority 8

########################################################################
# Create kluster run files (DONE - 2015-03-31 - Hiram)

    cd /hive/data/genomes/ornAna2
    # numerator is ornAna2 gapless bases "real" as reported by:
    head -1 faSize.ornAna2.2bit.txt
# 1996826513 bases (154575690 N's 1842250823 real 947687014 upper
#    894563809 lower) in 201525 sequences in 1 files

    # numerator is 'real' base count
    # 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 \( 1842250823 / 2861349177 \) \* 1024
    # ( 1842250823 / 2861349177 ) * 1024 = 659.292077

    # ==> use -repMatch=600 according to size scaled down from 1024 for human.
    #   and rounded down to nearest 50
    cd /hive/data/genomes/ornAna2
    time blat ornAna2.2bit \
         /dev/null /dev/null -tileSize=11 -makeOoc=jkStuff/ornAna2.11.ooc \
        -repMatch=600
    # Wrote 36683 overused 11-mers to jkStuff/ornAna2.11.ooc
    # real    0m43.465s

    # there are no non-bridged gaps, do not need to do this
    #   check non-bridged gaps to see what the typical size is:
#     hgsql -N -e 'select * from gap where bridge="no" order by size;' ornAna2
#       | ave -tableOut -col=7 stdin
# # min Q1 median Q3 max mean N sum stddev
# 50076 58368.8 70128 100495 1.07816e+07 178173 670 1.19376e+08 672006

    # note the minimum non-bridged gap size is 50,076

#  gapToLift -verbose=2 -minGap=50000 ornAna2 jkStuff/ornAna2.nonBridged.lft \
#         -bedFile=jkStuff/ornAna2.nonBridged.bed

#    hgsql -N \
#        -e 'select * from gap where bridge="no" order by size;' ornAna2 \
#        | ave -col=7 stdin

    # not needed:
#    gapToLift -verbose=2 -minGap=100 bosTau7 jkStuff/nonBridged.lft \
#        -bedFile=jkStuff/nonBridged.bed

    # survey sizes:
    n50.pl chrom.sizes
#       reading: chrom.sizes
#       contig count: 201525, total size: 1996826513, one half size: 998413256
# cumulative    N50 count       contig  contig size
# 997684181       181     chrUn_DS181652v1        992865
# 998413256 one half size
# 998675786       182     chrUn_DS181001v1        991605

##############################################################################
# LIFTOVER TO ornAna1 (DONE - 2015-06-19 - Hiram )
    mkdir /hive/data/genomes/ornAna2/bed/blat.ornAna1.2015-06-19
    cd /hive/data/genomes/ornAna2/bed/blat.ornAna1.2015-06-19
    # -debug run to create run dir, preview scripts...
    #	verifies files can be found
    doSameSpeciesLiftOver.pl -debug \
         -ooc=/hive/data/genomes/ornAna2/jkStuff/ornAna2.11.ooc ornAna2 ornAna1
    # Real run:
    time (doSameSpeciesLiftOver.pl -verbose=2 \
	-bigClusterHub=ku -dbHost=hgwdev -workhorse=hgwdev \
         -ooc=/hive/data/genomes/ornAna2/jkStuff/ornAna2.11.ooc \
	 ornAna2 ornAna1) > do.log 2>&1
    #	real    335m19.206s

    # verify the liftOver functions in the genome browser from ornAna2 to
    # ornAna1

#############################################################################
# GENBANK AUTO UPDATE (DONE - 2015-06-09 - Hiram)
    ssh hgwdev
    cd $HOME/kent/src/hg/makeDb/genbank
    git pull
    # /cluster/data/genbank/data/organism.lst shows:
    # #organism       mrnaCnt estCnt  refSeqCnt
    # Ornithorhynchus anatinus        293     9699    343

    # edit etc/genbank.conf to add ornAna2 just before ornAna1

# ornAna2 (Platypus -- Ornithorhynchus anatinus)
ornAna2.serverGenome = /hive/data/genomes/ornAna2/ornAna2.2bit
ornAna2.clusterGenome = /scratch/data/ornAna2/ornAna2.2bit
ornAna2.refseq.mrna.native.pslCDnaFilter  = ${lowCover.refseq.mrna.native.pslCDnaFilter}
ornAna2.refseq.mrna.xeno.pslCDnaFilter    = ${lowCover.refseq.mrna.xeno.pslCDnaFilter}
ornAna2.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter}
ornAna2.genbank.mrna.xeno.pslCDnaFilter   = ${lowCover.genbank.mrna.xeno.pslCDnaFilter}
ornAna2.genbank.est.native.pslCDnaFilter  = ${lowCover.genbank.est.native.pslCDnaFilter}
ornAna2.ooc = /scratch/data/ornAna2/11.ooc
ornAna2.lift = no
ornAna2.refseq.mrna.xeno.load  = yes
ornAna2.refseq.mrna.xeno.loadDesc = yes
# DO NOT NEED genbank.mrna.xeno except for human, mouse
ornAna2.genbank.mrna.xeno.load = no
ornAna2.downloadDir = ornAna2
ornAna2.perChromTables = no
# ornAna2.upstreamGeneTbl = ensGene
# ornAna2.upstreamMaf = multiz6way
# /hive/data/genomes/ornAna1/bed/multiz6way.2007-04-24/species.lst


    git commit -m "adding ornAna2 refs #15098" 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 ornAna2
    # logFile: var/build/logs/2015.05.22-11:39:57.ornAna2.initalign.log
    # real    209m45.611s

    #   To re-do, rm the dir first:
    #     /cluster/data/genbank/work/initial.ornAna2

    # load database when finished
    ssh hgwdev
    cd /cluster/data/genbank
    time ./bin/gbDbLoadStep -drop -initialLoad ornAna2
    # logFile: var/dbload/hgwdev/logs/2015.06.09-13:58:35.ornAna2.dbload.log
    # real    22m24.264s

    # enable daily alignment and update of hgwdev
    cd ~/kent/src/hg/makeDb/genbank
    git pull
    # add ornAna2 to:
    #   vi etc/align.dbs etc/hgwdev.dbs
    git commit -m "Added ornAna2 - platypus refs #15098" \
      etc/align.dbs etc/hgwdev.dbs
    git push
    make etc-update

#########################################################################
# all.joiner update, downloads and in pushQ - (DONE 2015-06-22 - Hiram)
    cd $HOME/kent/src/hg/makeDb/schema
    # fixup all.joiner until this is a clean output
    joinerCheck -database=ornAna2 -tableCoverage all.joiner
    joinerCheck -database=ornAna2 -times all.joiner
    joinerCheck -database=ornAna2 -keys all.joiner

    cd /hive/data/genomes/ornAna2
    time makeDownloads.pl ornAna2 > downloads.log 2>&1
    # real    16m40.268s

    #   now ready for pushQ entry
    mkdir /hive/data/genomes/ornAna2/pushQ
    cd /hive/data/genomes/ornAna2/pushQ
    makePushQSql.pl ornAna2 > ornAna2.pushQ.sql 2> stderr.out
    #   check for errors in stderr.out, some are OK, e.g.:
    #  WARNING: hgwdev does not have /gbdb/ornAna2/wib/gc5Base.wib
    #  WARNING: hgwdev does not have /gbdb/ornAna2/wib/quality.wib
    #  WARNING: hgwdev does not have /gbdb/ornAna2/bbi/qualityBw/quality.bw
    #  WARNING: ornAna2 does not have seq
    #  WARNING: ornAna2 does not have extFile

    #   copy it to hgwbeta
    scp -p ornAna2.pushQ.sql qateam@hgwbeta:/tmp
    ssh qateam@hgwbeta "./bin/x86_64/hgsql qapushq < /tmp/ornAna2.pushQ.sql"
    #   in that pushQ entry walk through each entry and see if the
    #   sizes will set properly

#########################################################################
# add chromAlias table (DONE - 2017-06-22 - Hiram)

    mkdir /hive/data/genomes/ornAna2/bed/chromAlias
    cd /hive/data/genomes/ornAna2/bed/chromAlias

    join ../idKeys/ornAna2.idKeys.txt \
 ../../genbank/idKeys/GCA_000002275.2_ASM227v2.idKeys.txt \
    | awk '{printf "%s\t%s\n", $2,$3}' | sort > ucsc.genbank.tab

    join ../idKeys/ornAna2.idKeys.txt \
 ../../refseq/refseq.idKeys.txt \
    | awk '{printf "%s\t%s\n", $2,$3}' | sort > ucsc.refseq.tab

    join ../idKeys/ornAna2.idKeys.txt \
 ../../ensembl/ensOrnAna.idKeys.txt \
    | awk '{printf "%s\t%s\n", $2,$3}' | sort > ucsc.ensembl.tab

    ~/kent/src/hg/utils/automation/chromAlias.pl

    hgLoadSqlTab ornAna2 chromAlias ~/kent/src/hg/lib/chromAlias.sql \
        ornAna2.chromAlias.tab

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