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

# This file describes browser build for the panPan3

#  Can use existing photograph (otherwise find one before starting here)

#########################################################################
#  Initial steps, reuse existing photograph (DONE - 2020-06-12 - Hiram)
# Might be a different individual, requests made

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

mkdir ~/kent/src/hg/makeDb/doc/panPan3
cd ~/kent/src/hg/makeDb/doc/panPan3

sed -e 's/gorGor6/panPan3/g; s/GorGor6/PanPan3/g; s/DONE/TBD/g;' \
  ../gorGor6/initialBuild.txt > initialBuild.txt

mkdir -p /hive/data/genomes/panPan3/refseq
cd /hive/data/genomes/panPan3

#  Can use existing photograph
cp -p ../panPan2/photoReference.txt ./
cat photoReference.txt
photoCreditURL  http://a-z-animals.com/animals/bonobo/pictures/2955/
photoCreditName Photo courtesy of Kabir Bakie

## download from NCBI
cd /hive/data/genomes/panPan3/refseq

time rsync -L -a -P --stats \
rsync://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/013/052/645/GCF_013052645.1_Mhudiblu_PPA_v0/ ./

# sent 3,203 bytes  received 6,058,365,683 bytes  56,886,092.83 bytes/sec
# total size is 6,056,874,807  speedup is 1.00

# real    1m45.870s

# this information is from the top of 
#    panPan3/refseq/*_assembly_report.txt
#    (aka: panPan3/refseq/GCF_013052645.1_Mhudiblu_PPA_v0_assembly_report.txt )

# Assembly name:  Mhudiblu_PPA_v0
# Organism name:  Pan paniscus (pygmy chimpanzee)
# Isolate:  Mhudiblu (Carbone #601152)
# Sex:  female
# Taxid:          9597
# BioSample:      SAMN11123633
# BioProject:     PRJNA526933
# Submitter:      University of Washington
# Date:           2020-05-15
# Assembly type:  haploid
# Release type:   major
# Assembly level: Chromosome
# Genome representation: full
# WGS project:    SSBP01
# Assembly method: FALCON v. (git hash: 91e700c4) Nov 2015
# Expected final version: no
# Genome coverage: 85.0x
# Sequencing technology: PacBio RSII; Illumina
# GenBank assembly accession: GCA_013052645.1
# RefSeq assembly accession: GCF_013052645.1
# RefSeq assembly and GenBank assemblies identical: no
#
## Assembly-Units:
## GenBank Unit Accession       RefSeq Unit Accession   Assembly-Unit name
## GCA_013052655.1      GCF_013052655.1 Primary Assembly
##      GCF_000029195.1 non-nuclear

# check assembly size for later reference:

faSize G*0_genomic.fna.gz

# 3051901337 bases (36551040 N's 3015350297 real 1802830734 upper
#	1212519563 lower) in 4293 sequences in 1 files
# Total size: mean 710901.8 sd 9447605.7 min 209 (NW_023258064.1)
#	max 224621958 (NC_048239.1) median 32647
# %39.73 masked total, %40.21 masked real

#############################################################################
# establish config.ra file (DONE - Hiram - 2020-06-12)
    cd /hive/data/genomes/panPan3
    ~/kent/src/hg/utils/automation/prepConfig.pl panPan3 mammal bonobo \
       refseq/*_assembly_report.txt > panPan3.config.ra

    # verify it is sane:
    diff panPan3.config.ra ../panPan2/panPan2.config.ra

    # fixup commonName, from:
commonName Pygmy chimpanzee
to
commonName Bonobo 

genomeCladePriority 35
to
genomeCladePriority 15

orderKey 17442
to
orderKey 2623

    # verify it really does look sane
    cat panPan3.config.ra
# config parameters for makeGenomeDb.pl:
db panPan3
clade mammal
genomeCladePriority 15
scientificName Pan paniscus
commonName Bonobo
assemblyDate May 2020
assemblyLabel University of Washington
assemblyShortLabel Mhudiblu_PPA_v0
orderKey 2623
# mitochondrial sequence included in refseq release
# mitoAcc NC_001644.1
mitoAcc none
fastaFiles /hive/data/genomes/panPan3/ucsc/*.fa.gz
agpFiles /hive/data/genomes/panPan3/ucsc/*.agp
# qualFiles none
dbDbSpeciesDir bonobo
photoCreditURL  http://a-z-animals.com/animals/bonobo/pictures/2955/
photoCreditName Photo courtesy of Kabir Bakie
ncbiGenomeId 10729
ncbiAssemblyId 7133581
ncbiAssemblyName Mhudiblu_PPA_v0
ncbiBioProject 526933
ncbiBioSample SAMN11123633
genBankAccessionID GCF_013052645.1
taxId 9597

#############################################################################
# setup UCSC named files (DONE - 2020-06-12 - Hiram)

    mkdir /hive/data/genomes/panPan3/ucsc
    cd /hive/data/genomes/panPan3/ucsc

    # check for duplicate sequences:
    time faToTwoBit -noMask ../refseq/G*0_genomic.fna.gz refseq.2bit
    #  real    0m44.404s


    twoBitDup refseq.2bit
    # no output is a good result, otherwise, would have to eliminate duplicates
    # the scripts creating the fasta here will be using this refseq.2bit file
    # remove it later

    time ~/kent/src/hg/utils/automation/ucscCompositeAgp.pl \
      ../refseq/G*0_genomic.fna.gz \
	../refseq/*_assembly_structure/Primary_Assembly
NC_048239.1 chr1
NC_048240.1 chr2A
NC_048241.1 chr2B
NC_048242.1 chr3
NC_048243.1 chr4
NC_048244.1 chr5
NC_048245.1 chr6
NC_048246.1 chr7
NC_048247.1 chr8
NC_048248.1 chr9
NC_048249.1 chr10
NC_048250.1 chr11
NC_048251.1 chr12
NC_048252.1 chr13
NC_048253.1 chr14
NC_048254.1 chr15
NC_048255.1 chr16
NC_048256.1 chr17
NC_048257.1 chr18
NC_048258.1 chr19
NC_048259.1 chr20
NC_048260.1 chr21
NC_048261.1 chr22
NC_048262.1 chrX

# real    11m31.473s

    time ~/kent/src/hg/utils/automation/unplacedWithChroms.pl \
       ../refseq/*_assembly_structure/Primary_Assembly
    # processed 4268 sequences into chrUn.fa.gz
    # real    0m50.843s

    # there are *no* unlocalized sequences
    time ~/kent/src/hg/utils/automation/unlocalizedWithChroms.pl \
       ../refseq/*_assembly_structure/Primary_Assembly

    # bash syntax here
    mitoAcc=`grep "^# mitoAcc" ../panPan3.config.ra | awk '{print $NF}'`
    printf "# mitoAcc %s\n" "$mitoAcc"
# mitoAcc NC_001644.1

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

    cat chrM.agp
# chrM    1       16563   1       O       NC_001644.1     1       16563   +

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

    faSize chrM.fa.gz
# 16563 bases (0 N's 16563 real 16563 upper 0 lower) in 1 sequences in 1 files

    # verify fasta and AGPs agree
    time faToTwoBit *.fa.gz test.2bit
    # real    0m55.327s

    cat *.agp | checkAgpAndFa stdin test.2bit 2>&1 | tail -4
    # All AGP and FASTA entries agree - both files are valid

    # and no sequence lost from orginal:
    twoBitToFa test.2bit stdout | faSize stdin
# 3051901337 bases (36551040 N's 3015350297 real 3015350297 upper
#	0 lower) in 4293 sequences in 1 files

    # same numbers as above (except for upper/lower masking)
# 3051901337 bases (36551040 N's 3015350297 real 1802830734 upper
#	1212519563 lower) in 4293 sequences in 1 files

    # no longer need these temporary 2bit files
    rm test.2bit refseq.2bit

#############################################################################
#  Initial database build (DONE - 2020-06-12 - Hiram)

    # verify sequence and AGP are OK:
    cd /hive/data/genomes/panPan3
    time (makeGenomeDb.pl -workhorse=hgwdev -dbHost=hgwdev -fileServer=hgwdev \
         -stop=agp panPan3.config.ra) > agp.log 2>&1
    # real    2m32.140s

    # then finish it off:
    time (makeGenomeDb.pl -workhorse=hgwdev -dbHost=hgwdev \
       -fileServer=hgwdev -continue=db panPan3.config.ra) > db.log 2>&1
    # real    16m31.749s

    # fixing trackDb step:  (new files required in trackDb source fetch)
    time (~/kent/src/hg/utils/automation/makeGenomeDb.pl -workhorse=hgwdev \
      -dbHost=hgwdev -continue=trackDb -fileServer=hgwdev \
         panPan3.config.ra) > trackDb.log 2>&1
    # real    0m6.470s

    # check in the trackDb files created in TemporaryTrackDbCheckout/
    #    and add panPan3 to trackDb/makefile

    # temporary symlink until masked sequence is available
    cd /hive/data/genomes/panPan3
    ln -s `pwd`/panPan3.unmasked.2bit /gbdb/panPan3/panPan3.2bit

#############################################################################
# check gap table vs NCBI gap file (DONE - 2020-06-12 - Hiram)
    mkdir /hive/data/genomes/panPan3/bed/gap
    cd /hive/data/genomes/panPan3/bed/gap

    zgrep -v "^#" ../../refseq/G*_gaps.txt.gz \
	| awk '{printf "%s\t%d\t%d\t%s_%s\n", $1,$2-1,$3,$5,$6}' \
	| sort -k1,1 -k2,2n > refseq.gap.bed

    # type survey:
    cut -f4 *.bed | sort | uniq -c
    #     64 between_scaffolds_na
    #    619 within_scaffold_map

    # how much defined by NCBI:
    awk '{print $3-$2}' *.bed | ave stdin | grep -w total
    # total 36551040.000000

    # how much in the gap table:
    hgsql -e 'select * from gap;' panPan3 | awk '{print $4-$3}' \
	| ave stdin | grep -w total
    # total 36551040.000000

    # equal amounts, no need to adjust the gap table

##############################################################################
# cpgIslands on UNMASKED sequence (DONE - 2020-06-12 - Hiram)
    mkdir /hive/data/genomes/panPan3/bed/cpgIslandsUnmasked
    cd /hive/data/genomes/panPan3/bed/cpgIslandsUnmasked

    time (doCpgIslands.pl -dbHost=hgwdev -bigClusterHub=ku -buildDir=`pwd` \
       -tableName=cpgIslandExtUnmasked \
          -maskedSeq=/hive/data/genomes/panPan3/panPan3.unmasked.2bit \
             -workhorse=hgwdev -smallClusterHub=ku panPan3) > do.log 2>&1
    # real    4m48.939s

    cat fb.panPan3.cpgIslandExtUnmasked.txt
    # 29049864 bases of 3015350297 (0.963%) in intersection

#############################################################################
# cytoBandIdeo - (DONE - 2020-06-12 - Hiram)
    mkdir /hive/data/genomes/panPan3/bed/cytoBand
    cd /hive/data/genomes/panPan3/bed/cytoBand
    makeCytoBandIdeo.csh panPan3

#############################################################################
# run up idKeys files for chromAlias/ncbiRefSeq (DONE - 2020-06-12 - Hiram)
    mkdir /hive/data/genomes/panPan3/bed/idKeys
    cd /hive/data/genomes/panPan3/bed/idKeys

    time (doIdKeys.pl \
        -twoBit=/hive/data/genomes/panPan3/panPan3.unmasked.2bit \
        -buildDir=`pwd` panPan3) > do.log 2>&1 &
    # real    22m22.873s

    cat panPan3.keySignature.txt
    #  25a9ac3ecf4f0b51c5a213bd22ddd73f

#############################################################################
# gapOverlap (DONE - 2020-06-12 - Hiram)
    mkdir /hive/data/genomes/panPan3/bed/gapOverlap
    cd /hive/data/genomes/panPan3/bed/gapOverlap
    time (doGapOverlap.pl \
        -twoBit=/hive/data/genomes/panPan3/panPan3.unmasked.2bit panPan3 ) \
        > do.log 2>&1 &
    # real    1m49.512s

    # there is only one:
    wc -l bed.tab
    # 1 bed.tab
    cut -f2- bed.tab
#chr7    144505525       144507630       chr7:144505526-144507630    803    +
#            144505525       144507630       0       2       803,803 0,1302

    cat fb.panPan3.gapOverlap.txt
    # 1606 bases of 3051901337 (0.000%) in intersection

#############################################################################
# tandemDups (DONE - 2020-06-12 - Hiram)
    mkdir /hive/data/genomes/panPan3/bed/tandemDups
    cd /hive/data/genomes/panPan3/bed/tandemDups
    time (~/kent/src/hg/utils/automation/doTandemDup.pl \
  -twoBit=/hive/data/genomes/panPan3/panPan3.unmasked.2bit panPan3) \
        > do.log 2>&1 &
    # real    188m31.667s

    cat fb.panPan3.tandemDups.txt
    # 158351117 bases of 3051901337 (5.189%) in intersection

    bigBedInfo panPan3.tandemDups.bb | sed -e 's/^/#  /;'
#  version: 4
#  fieldCount: 13
#  hasHeaderExtension: yes
#  isCompressed: yes
#  isSwapped: 0
#  extraIndexCount: 0
#  itemCount: 3,019,527
#  primaryDataSize: 77,104,242
#  primaryIndexSize: 283,772
#  zoomLevels: 9
#  chromCount: 4151
#  basesCovered: 1,653,271,326
#  meanDepth (of bases covered): 15.653055
#  minDepth: 1.000000
#  maxDepth: 425.000000
#  std of depth: 34.287645

#########################################################################
# ucscToINSDC and ucscToRefSeq table/track (DONE - 2020-06-12 - Hiram)
    # construct idKeys for the refseq sequence
    mkdir /hive/data/genomes/panPan3/refseq/idKeys
    cd /hive/data/genomes/panPan3/refseq/idKeys
    faToTwoBit ../GCF_*0_genomic.fna.gz panPan3.refSeq.2bit

    time (doIdKeys.pl -buildDir=`pwd` \
        -twoBit=`pwd`/panPan3.refSeq.2bit refseqPanPan3)  > do.log 2>&1 &
    # real    6m11.312s

    cat refseqPanPan3.keySignature.txt
    #  25a9ac3ecf4f0b51c5a213bd22ddd73f

    # and the genbank sequence needs keys too:
    mkdir /hive/data/genomes/panPan3/refseq/idKeysGenbank
    cd /hive/data/genomes/panPan3/refseq/idKeysGenbank
    faToTwoBit /hive/data/outside/ncbi/genomes/GCA/013/052/645/GCA_013052645.1_Mhudiblu_PPA_v0/GCA_013052645.1_Mhudiblu_PPA_v0_genomic.fna.gz panPan3.genbank.2bit

    time (doIdKeys.pl -buildDir=`pwd` \
        -twoBit=`pwd`/panPan3.genbank.2bit genbankPanPan3)  > do.log 2>&1 &
    # real    12m24.596s

    cat genbankPanPan3.keySignature.txt
    #  8fd9bb74aebe493c87e8a961a031ba3f

    mkdir /hive/data/genomes/panPan3/bed/chromAlias
    cd /hive/data/genomes/panPan3/bed/chromAlias

    join -t$'\t' ../idKeys/panPan3.idKeys.txt \
        ../../refseq/idKeysGenbank/genbankPanPan3.idKeys.txt | cut -f2- \
          | sort -k1,1 | join -t$'\t' <(sort -k1,1 ../../chrom.sizes) - \
            | awk '{printf "%s\t0\t%d\t%s\n", $1, $2, $3}' \
               | sort -k1,1 -k2,2n > ucscToINSDC.bed

    join -t$'\t' ../idKeys/panPan3.idKeys.txt \
        ../../refseq/idKeys/refseqPanPan3.idKeys.txt | cut -f2- \
          | sort -k1,1 | join -t$'\t' <(sort -k1,1 ../../chrom.sizes) - \
            | awk '{printf "%s\t0\t%d\t%s\n", $1, $2, $3}' \
               | sort -k1,1 -k2,2n > ucscToRefSeq.bed

    # should be same line counts throughout:
    wc -l * ../../chrom.sizes
    #	4292 ucscToINSDC.bed
    #	4293 ucscToRefSeq.bed
    #	4293 ../../chrom.sizes

    # need to find the accession for the INSDC equivalent to chrM:
    egrep chrM *
# refSeq.bed:chrM   0       16563   NC_001644.1

    # lookup that accession at NCBI Entrez: D38116.1
    # and add to ucscToINSDC.bed:
    printf "chrM\t0\t16563\tD38116.1\n" >> ucscToINSDC.bed
    # verify:
    grep chrM *
ucscToINSDC.bed:chrM    0       16563   D38116.1
ucscToRefSeq.bed:chrM   0       16563   NC_001644.1

    export chrSize=`cut -f1 ucscToINSDC.bed | awk '{print length($0)}' | sort -n | tail -1`
    echo $chrSize
    # 20
    # use the $chrSize in this sed
    sed -e "s/21/$chrSize/" $HOME/kent/src/hg/lib/ucscToINSDC.sql \
         | hgLoadSqlTab panPan3 ucscToINSDC stdin ucscToINSDC.bed
     # should be the same for ucscToRefSeq:
    export chrSize=`cut -f1 ucscToRefSeq.bed | awk '{print length($0)}' | sort -n | tail -1`
    echo $chrSize
    # 26
    sed -e "s/21/$chrSize/" $HOME/kent/src/hg/lib/ucscToINSDC.sql \
       | sed -e 's/INSDC/RefSeq/g;' \
         | hgLoadSqlTab panPan3 ucscToRefSeq stdin ucscToRefSeq.bed

    # should be quiet for all OK
    checkTableCoords panPan3

    # should cover %100 entirely:
    featureBits -countGaps panPan3 ucscToINSDC
    # 3051901337 bases of 3051901337 (100.000%) in intersection
    featureBits -countGaps panPan3 ucscToRefSeq
    # 3051901337 bases of 3051901337 (100.000%) in intersection

#########################################################################
# add chromAlias table (DONE - 2020-06-12 - Hiram)

    mkdir /hive/data/genomes/panPan3/bed/chromAlias
    cd /hive/data/genomes/panPan3/bed/chromAlias

    hgsql -N -e 'select chrom,name from ucscToRefSeq;' panPan3 \
        | sort -k1,1 > ucsc.refseq.tab
    hgsql -N -e 'select chrom,name from ucscToINSDC;' panPan3 \
        | sort -k1,1 > ucsc.genbank.tab

    grep -v "^#" \
      ../../refseq/G*0_assembly_report.txt \
       | awk -F$'\t' '{printf "%s\t%s\n", $7,$1}' \
         | sort > refseq.assembly.txt

    # do *not* need the ones that have identical names to UCSC names
    join -2 2 -t$'\t' refseq.assembly.txt <(sort -k2,2 ucsc.refseq.tab) \
      | awk -F$'\t' '{printf "%s\t%s\n", $3, $2}' \
        | awk -F$'\t' '$1 != $2' | sort > ucsc.assembly.tab

    wc -l *.tab | sed -e 's/^/#   /;'
#     4293 ucsc.genbank.tab
#     4293 ucsc.refseq.tab
#     4271 ucsc.assembly.tab

    ~/kent/src/hg/utils/automation/chromAlias.pl ucsc.*.tab \
        > panPan3.chromAlias.tab

for t in refseq genbank assembly
do
  c0=`cat ucsc.$t.tab | wc -l`
  c1=`grep $t panPan3.chromAlias.tab | wc -l`
  ok="OK"
  if [ "$c0" -ne "$c1" ]; then
     ok="ERROR"
  fi
  printf "# checking $t: $c0 =? $c1 $ok\n"
done
# checking refseq: 4293 =? 4293 OK
# checking genbank: 4293 =? 4293 OK
# # checking assembly: 4271 =? 4271 OK

    # verify chrM is here properly:
    grep chrM panPan3.chromAlias.tab  | sed -e 's/^/# /;'
# D38116.1        chrM    genbank
# MT      chrM    assembly
# NC_001644.1     chrM    refseq

    hgLoadSqlTab panPan3 chromAlias ~/kent/src/hg/lib/chromAlias.sql \
        panPan3.chromAlias.tab

#########################################################################
# fixup search rule for assembly track/gold table (DONE - 2020-06-12 - Hiram)
    cd ~/kent/src/hg/makeDb/trackDb/bonobo/panPan3
    # preview prefixes and suffixes:
    hgsql -N -e "select frag from gold;" panPan3 \
      | sed -e 's/[0-9][0-9]*//;' | sort | uniq -c | sed -e 's/^/#  /;'
#        1 NC_.1
#     4975 SSBP.1

    # implies a rule: '[NS][CS][B0-9_][P0-9][0-9]+(\.[0-9]+)?'

    # verify this rule will find them all and eliminate them all:
    hgsql -N -e "select frag from gold;" panPan3 | wc -l
    # 4976

    hgsql -N -e "select frag from gold;" panPan3 \
       | egrep -e '[NS][CS][B0-9_][P0-9][0-9]+(\.[0-9]+)?' | wc -l
    # 4976

    hgsql -N -e "select frag from gold;" panPan3 \
       | egrep -v -e '[NS][CS][B0-9_][P0-9][0-9]+(\.[0-9]+)?' | wc -l
    # 0

    # hence, add to trackDb/rhesus/panPan3/trackDb.ra
searchTable gold
shortCircuit 1
termRegex [NS][CS][B0-9_][P0-9][0-9]+(\.[0-9]+)?
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 - 2020-06-12 - Hiram)
    mkdir /hive/data/genomes/panPan3/bed/repeatMasker
    cd /hive/data/genomes/panPan3/bed/repeatMasker
    time  (doRepeatMasker.pl -buildDir=`pwd` \
        -bigClusterHub=ku -dbHost=hgwdev -workhorse=hgwdev \
        -smallClusterHub=ku panPan3) > do.log 2>&1
    # real    420m57.419s

    cat faSize.rmsk.txt
# 3051901337 bases (36551040 N's 3015350297 real 1503559806 upper
#	1511790491 lower) in 4293 sequences in 1 files
# Total size: mean 710901.8 sd 9447605.7 min 209 (chrUn_NW_023258064v1)
#	max 224621958 (chr1) median 32647
# %49.54 masked total, %50.14 masked real

# Original masking from NCBI:
# %39.73 masked total, %40.21 masked real

    egrep -i "versi|relea" do.log
# RepeatMasker version development-$Id: RepeatMasker,v 1.332 2017/04/17 19:01:11 rhubley Exp $
# CC    Dfam_Consensus RELEASE 20181026;                            *
# CC    RepBase RELEASE 20181026;          
# February 01 2017 (open-4-0-8) 1.332 version of RepeatMasker

    time featureBits -countGaps panPan3 rmsk
    #	1511789076 bases of 3051901337 (49.536%) in intersection
    #	real    0m51.367s

    # why is it different than the faSize above ?
    # because rmsk masks out some N's as well as bases, the faSize count above
    #   separates out the N's from the bases, it doesn't show lower case N's

    # faster way to get the same result on high contig count assemblies:
    time hgsql -N -e 'select genoName,genoStart,genoEnd from rmsk;' panPan3 \
        | bedSingleCover.pl stdin | ave -col=4 stdin | grep "^total"
    # total 1511789076.000000
    # real    0m22.577s

##########################################################################
# running simple repeat (DONE - 2020-06-12 - Hiram)

    mkdir /hive/data/genomes/panPan3/bed/simpleRepeat
    cd /hive/data/genomes/panPan3/bed/simpleRepeat
    time (doSimpleRepeat.pl -buildDir=`pwd` -bigClusterHub=ku \
        -dbHost=hgwdev -workhorse=hgwdev -smallClusterHub=ku \
        -trf409=6 panPan3) > do.log 2>&1
    # real    328m38.113s

    cat fb.simpleRepeat
    # 256626302 bases of 3015350297 (8.511%) in intersection

    cd /hive/data/genomes/panPan3
    # using the Window Masker result:
    cd /hive/data/genomes/panPan3
#    twoBitMask bed/windowMasker/panPan3.cleanWMSdust.2bit \
#       -add bed/simpleRepeat/trfMask.bed  panPan3.2bit
    #   you can safely ignore the warning about fields >= 13

    # add to rmsk after it is done:
    twoBitMask panPan3.rmsk.2bit \
        -add bed/simpleRepeat/trfMask.bed panPan3.2bit
    #   you can safely ignore the warning about fields >= 13
    twoBitToFa panPan3.2bit stdout | faSize stdin > faSize.panPan3.2bit.txt
    cat faSize.panPan3.2bit.txt
# 3051901337 bases (36551040 N's 3015350297 real 1501255487 upper
#	1514094810 lower) in 4293 sequences in 1 files
# Total size: mean 710901.8 sd 9447605.7 min 209 (chrUn_NW_023258064v1)
#	max 224621958 (chr1) median 32647
# %49.61 masked total, %50.21 masked real

    rm /gbdb/panPan3/panPan3.2bit
    ln -s `pwd`/panPan3.2bit /gbdb/panPan3/panPan3.2bit

#########################################################################
# CREATE MICROSAT TRACK (DONE - 2020-06-13 - Hiram)
    ssh hgwdev
    mkdir /cluster/data/panPan3/bed/microsat
    cd /cluster/data/panPan3/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 panPan3 microsat microsat.bed
    # Read 27378 elements of size 4 from microsat.bed

##########################################################################
## WINDOWMASKER (DONE - 2020-06-12 - Hiram)

    mkdir /hive/data/genomes/panPan3/bed/windowMasker
    cd /hive/data/genomes/panPan3/bed/windowMasker
    time (doWindowMasker.pl -buildDir=`pwd` -workhorse=hgwdev \
        -dbHost=hgwdev panPan3) > do.log 2>&1
    # real    131m20.699s

    # Masking statistics
    cat faSize.panPan3.cleanWMSdust.txt
# 3051901337 bases (36551040 N's 3015350297 real 1785076452 upper
#	1230273845 lower) in 4293 sequences in 1 files
# Total size: mean 710901.8 sd 9447605.7 min 209 (chrUn_NW_023258064v1)
#	max 224621958 (chr1) median 32647
# %40.31 masked total, %40.80 masked real

    cat fb.panPan3.rmsk.windowmaskerSdust.txt
    # 882436977 bases of 3051901337 (28.914%) in intersection

##########################################################################
# cpgIslands - (DONE - 2020-06-15 - Hiram)
    mkdir /hive/data/genomes/panPan3/bed/cpgIslands
    cd /hive/data/genomes/panPan3/bed/cpgIslands
    time (doCpgIslands.pl -dbHost=hgwdev -bigClusterHub=ku \
      -workhorse=hgwdev -smallClusterHub=ku panPan3) > do.log 2>&1
    # real    4m8.773s

    cat fb.panPan3.cpgIslandExt.txt
    # 21946791 bases of 3015350297 (0.728%) in intersection

##############################################################################
# genscan - (DONE - 2020-06-15 - Hiram)
    mkdir /hive/data/genomes/panPan3/bed/genscan
    cd /hive/data/genomes/panPan3/bed/genscan
    time (doGenscan.pl -buildDir=`pwd` -workhorse=hgwdev -dbHost=hgwdev \
      -bigClusterHub=ku panPan3) > do.log 2>&1
    # real    250m19.909s

    cat fb.panPan3.genscan.txt
    # 53138526 bases of 3015350297 (1.762%) in intersection

    cat fb.panPan3.genscanSubopt.txt
    # 51253170 bases of 3015350297 (1.700%) in intersection

#########################################################################
# Create kluster run files (DONE - 2020-06-15 - Hiram)

    # numerator is panPan3 gapless bases "real" as reported by:
    featureBits -noRandom -noHap panPan3 gap
    # 30700245 bases of 2756992444 (1.114%) 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 \( 2756992444 / 2861349177 \) \* 1024
    #  ( 2756992444 / 2861349177 ) * 1024 = 986.653529

    # ==> use -repMatch=950 according to size scaled down from 1024 for human.
    #   and rounded down to nearest 50
    cd /hive/data/genomes/panPan3
    time blat panPan3.2bit \
         /dev/null /dev/null -tileSize=11 -makeOoc=jkStuff/panPan3.11.ooc \
         -repMatch=950
    #   Wrote 40152 overused 11-mers to jkStuff/panPan3.11.ooc

    # panPan2 repMatch=900:
    #   Wrote 34618 overused 11-mers to jkStuff/panPan2.11.ooc
    # panPan1 repMatch=950:
    #  Wrote 31225 overused 11-mers to jkStuff/panPan1.11.ooc

    #   check non-bridged gaps to see what the typical size is:
    hgsql -N \
        -e 'select * from gap where bridge="no" order by size;' panPan3 \
        | sort -k7,7nr | ave -col=7 stdin
    # min 100.000000
    # max 100.000000
    # they are all 100 sized, 64 gaps

    # minimum gap size is 100 and produces a reasonable number of lifts
    gapToLift -verbose=2 -minGap=100 panPan3 jkStuff/panPan3.nonBridged.lft \
        -bedFile=jkStuff/panPan3.nonBridged.bed
    wc -l jkStuff/panPan3.nonBri*
    #	4357 jkStuff/panPan3.nonBridged.bed
    #	4357 jkStuff/panPan3.nonBridged.lft

##############################################################################
# GENBANK AUTO UPDATE (DONE - 2020-06-15 - Hiram)
    ssh hgwdev
    cd $HOME/kent/src/hg/makeDb/genbank
    git pull
    # /cluster/data/genbank/data/organism.lst shows:
    # organism       mrnaCnt estCnt  refSeqCnt
    # Pan paniscus    557     0       49

    # edit etc/genbank.conf to add panPan3 just before panPan2

# panPan3 (bonobo - Pan paniscus - GCF_013052645.1 Mhudiblu_PPA_v0 15 May 2020)
panPan3.serverGenome = /hive/data/genomes/panPan3/panPan3.2bit
panPan3.ooc = /hive/data/genomes/panPan3/jkStuff/panPan3.11.ooc
panPan3.lift = /hive/data/genomes/panPan3/jkStuff/panPan3.nonBridged.lft
panPan3.perChromTables = no
panPan3.refseq.mrna.native.pslCDnaFilter  = ${finished.refseq.mrna.native.pslCDnaFilter}
panPan3.refseq.mrna.xeno.pslCDnaFilter    = ${finished.refseq.mrna.xeno.pslCDnaFilter}
panPan3.genbank.mrna.native.pslCDnaFilter = ${finished.genbank.mrna.native.pslCDnaFilter}
panPan3.genbank.mrna.xeno.pslCDnaFilter   = ${finished.genbank.mrna.xeno.pslCDnaFilter}
panPan3.genbank.est.native.pslCDnaFilter  = ${finished.genbank.est.native.pslCDnaFilter}
panPan3.genbank.est.xeno.pslCDnaFilter    = ${finished.genbank.est.xeno.pslCDnaFilter}
panPan3.downloadDir = panPan3
# defaults yes genbank.mrna.native, genbank.est.native.load,
#              refseq.mrna.native, refseq.mrna.xeno
# DO NOT NEED genbank.mrna.xeno except for human, mouse
panPan3.genbank.est.native.load = no

    # verify the files specified exist before checking in the file:
  grep ^panPan3 etc/genbank.conf | grep hive | awk '{print $NF}' | xargs ls -og
# -rw-rw-r-- 1    160616 Jun 15 09:11 /hive/data/genomes/panPan3/jkStuff/panPan3.11.ooc
# -rw-rw-r-- 1    254979 Jun 15 09:13 /hive/data/genomes/panPan3/jkStuff/panPan3.nonBridged.lft
# -rw-rw-r-- 1 795168110 Jun 13 10:06 /hive/data/genomes/panPan3/panPan3.2bit

    git commit -m "Added panPan3 bonobo; refs #25720" etc/genbank.conf
    git push

    # update /cluster/data/genbank/:
    make etc-update

    # enable daily alignment and update of hgwdev
    cd ~/kent/src/hg/makeDb/genbank
    git pull
    # add panPan3 to:
    #   etc/hgwdev.dbs etc/align.dbs
    git commit -m "Added panPan3 - bonobo refs #25720" etc/hgwdev.dbs etc/align.dbs
    git push
    make etc-update

    # wait a few days for genbank magic to take place, the tracks will
    # appear

########################################################################
# lastz/chain/net swap human/hg38 (DONE - 2020-06-15 - Hiram)

    # original alignment
    cd /hive/data/genomes/hg38/bed/lastzPanPan3.2020-06-15

    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/chain/net swap mouse/mm10 (DONE - 2020-06-15 - Hiram)

    # original alignment
    cd /hive/data/genomes/mm10/bed/lastzPanPan3.2020-06-15

    cat fb.mm10.chainPanPan3Link.txt
    # 935579510 bases of 2652783500 (35.268%) in intersection
    cat fb.mm10.chainSynPanPan3Link.txt
    # 888900388 bases of 2652783500 (33.508%) in intersection

    time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` mm10 panPan3) \
      > rbest.log 2>&1 &
    # real    329m28.051s
    cat fb.mm10.chainRBest.PanPan3.txt
    # 890894306 bases of 2652783500 (33.583%) in intersection

    # and for the swap:
    mkdir /hive/data/genomes/panPan3/bed/blastz.mm10.swap
    cd /hive/data/genomes/panPan3/bed/blastz.mm10.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/mm10/bed/lastzPanPan3.2020-06-15/DEF \
        -swap -chainMinScore=3000 -chainLinearGap=medium \
          -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    #  real    55m23.982s

    cat fb.panPan3.chainMm10Link.txt
    # 954214151 bases of 3015350297 (31.645%) in intersection
    cat fb.panPan3.chainSynMm10Link.txt
    # 887980807 bases of 3015350297 (29.449%) in intersection

    time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` panPan3 mm10) \
       > rbest.log 2>&1
    # real    305m11.756s

    cat fb.panPan3.chainRBest.Mm10.txt
    # 889360051 bases of 3015350297 (29.494%) in intersection

##############################################################################
# augustus gene track (DONE - 2020-06-15 - Hiram)

    mkdir /hive/data/genomes/panPan3/bed/augustus
    cd /hive/data/genomes/panPan3/bed/augustus
    time (doAugustus.pl -buildDir=`pwd` -bigClusterHub=ku \
        -species=human -dbHost=hgwdev \
           -workhorse=hgwdev panPan3) > do.log 2>&1
    # real    124m57.738s

    cat fb.panPan3.augustusGene.txt
    # 55220084 bases of 3015350297 (1.831%) in intersection

#########################################################################
# ncbiRefSeq (DONE - 2020-06-13 - Hiram)

    mkdir /hive/data/genomes/panPan3/bed/ncbiRefSeq.2020-06-13
    cd /hive/data/genomes/panPan3/bed/ncbiRefSeq.2020-06-13
    time (~/kent/src/hg/utils/automation/doNcbiRefSeq.pl -buildDir=`pwd` \
      -bigClusterHub=ku -dbHost=hgwdev \
      -fileServer=hgwdev -smallClusterHub=hgwdev -workhorse=hgwdev \
      GCF_013052645.1_Mhudiblu_PPA_v0 panPan3) > do.log 2>&1 &
    # real    5m43.954s

    cat fb.ncbiRefSeq.panPan3.txt
    #  91843495 bases of 3015350297 (3.046%) in intersection

    # add: include ../../refSeqComposite.ra alpha
    # to the bonobo/panPan3/trackDb.ra to turn on the track in the browser

    featureBits -enrichment panPan3 refGene ncbiRefSeq 
 # refGene 0.004%, ncbiRefSeq 3.046%, both 0.004%, cover 99.99%, enrich 32.83x

    featureBits -enrichment panPan3 ncbiRefSeq refGene
 # ncbiRefSeq 3.046%, refGene 0.004%, both 0.004%, cover 0.11%, enrich 32.83x

    featureBits -enrichment panPan3 ncbiRefSeqCurated refGene
 # ncbiRefSeqCurated 0.004%, refGene 0.004%, both 0.003%, cover 90.24%, enrich 25764.34x

    featureBits -enrichment panPan3 refGene ncbiRefSeqCurated
 # refGene 0.004%, ncbiRefSeqCurated 0.004%, both 0.003%, cover 99.48%, enrich 25764.34x

#########################################################################
# LIFTOVER TO panPan2 (DONE - 2020-06-15 - Hiram)
    ssh hgwdev
    mkdir /hive/data/genomes/panPan3/bed/blat.panPan2.2020-06-15
    cd /hive/data/genomes/panPan3/bed/blat.panPan2.2020-06-15
    doSameSpeciesLiftOver.pl -verbose=2 \
        -debug -bigClusterHub=ku -dbHost=hgwdev -workhorse=hgwdev \
        -ooc=/hive/data/genomes/panPan3/jkStuff/panPan3.11.ooc \
         panPan3 panPan2
    time (doSameSpeciesLiftOver.pl -verbose=2 \
        -bigClusterHub=ku -dbHost=hgwdev -workhorse=hgwdev \
        -ooc=/hive/data/genomes/panPan3/jkStuff/panPan3.11.ooc \
         panPan3 panPan2) > doLiftOverToPanPan2.log 2>&1
    # real    273m17.026s

    # see if the liftOver menus function in the browser from panPan3 to panPan2

#########################################################################
# LIFTOVER TO panPan1 (DONE - 2020-06-15 - Hiram)
    ssh hgwdev
    mkdir /hive/data/genomes/panPan3/bed/blat.panPan1.2020-06-15
    cd /hive/data/genomes/panPan3/bed/blat.panPan1.2020-06-15
    doSameSpeciesLiftOver.pl -verbose=2 \
        -debug -bigClusterHub=ku -dbHost=hgwdev -workhorse=hgwdev \
        -ooc=/hive/data/genomes/panPan3/jkStuff/panPan3.11.ooc \
         panPan3 panPan1
    time (doSameSpeciesLiftOver.pl -verbose=2 \
        -bigClusterHub=ku -dbHost=hgwdev -workhorse=hgwdev \
        -ooc=/hive/data/genomes/panPan3/jkStuff/panPan3.11.ooc \
         panPan3 panPan1) > doLiftOverToPanPan1.log 2>&1
    # real    275m17.469s

    # see if the liftOver menus function in the browser from panPan3 to panPan1

#########################################################################
#  BLATSERVERS ENTRY (DONE - 2020-06-16 - 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 ("panPan3", "blat1a", "17900", "1", "0"); \
	INSERT INTO blatServers (db, host, port, isTrans, canPcr) \
	VALUES ("panPan3", "blat1a", "17901", "0", "1");' \
	    hgcentraltest
    #	test it with some sequence

############################################################################
## reset default position similar to panPan2 found via blat of FOXP2 protein
##  (DONE - 2020-06-16 - Hiram)

    ssh hgwdev
    hgsql -e 'update dbDb set defaultPos="chr7:106336524-106733879"
	where name="panPan3";' hgcentraltest


##############################################################################
# crispr whole genome (DONE - 2020-06-15 - Hiram)
    mkdir /hive/data/genomes/panPan3/bed/crisprAll
    cd /hive/data/genomes/panPan3/bed/crisprAll

    # the large shoulder argument will cause the entire genome to be scanned
    # this takes a while for a new genome to get the bwa indexing done
    time (~/kent/src/hg/utils/automation/doCrispr.pl -verbose=2 -stop=ranges \
       panPan3 ncbiRefSeq -shoulder=250000000 -tableName=crisprAll \
         -fileServer=hgwdev -buildDir=`pwd` -smallClusterHub=hgwdev \
           -bigClusterHub=ku \
              -workhorse=hgwdev) > ranges.log 2>&1
    # real    80m34.161s

    time (~/kent/src/hg/utils/automation/doCrispr.pl -verbose=2 \
       -continue=guides -stop=specScores panPan3 ncbiRefSeq \
	-shoulder=250000000 -tableName=crisprAll -fileServer=hgwdev \
    -buildDir=`pwd` -smallClusterHub=hgwdev -bigClusterHub=ku \
      -workhorse=hgwdev) > specScores.log 2>&1
    # Number of specScores: 232496133
    # real    6369m47.263s

    cat guides/run.time | sed -e 's/^/# /;'
# Completed: 100 of 100 jobs
# CPU time in finished jobs:      17860s     297.67m     4.96h    0.21d  0.001 y
# IO & Wait Time:                   389s       6.48m     0.11h    0.00d  0.000 y
# Average job time:                 182s       3.04m     0.05h    0.00d
# Longest finished job:             575s       9.58m     0.16h    0.01d
# Submission to last job:           583s       9.72m     0.16h    0.01d

    cat specScores/run.time | sed -e 's/^/# /;'
# Completed: 3104861 of 3104861 jobs
# CPU time in finished jobs:  310874778s 5181246.29m 86354.10h 3598.09d  9.858 y
# IO & Wait Time:               8751069s  145851.16m  2430.85h  101.29d  0.277 y
# Average job time:                 103s       1.72m     0.03h    0.00d
# Longest finished job:             414s       6.90m     0.12h    0.00d
# Submission to last job:        314519s    5241.98m    87.37h    3.64d


    ### remember to get back to hgwdev to run this
    time (~/kent/src/hg/utils/automation/doCrispr.pl -verbose=2 \
       -continue=effScores -stop=load panPan3 ncbiRefSeq \
    -shoulder=250000000 -tableName=crisprAll -fileServer=hgwdev \
    -buildDir=`pwd` -smallClusterHub=hgwdev -bigClusterHub=ku \
      -workhorse=hgwdev) > load.log 2>&1
    # real    1633m51.680s

    cat effScores/run.time | sed -e 's/^/# /;'
# Completed: 28661 of 28661 jobs
# CPU time in finished jobs:   13143908s  219065.14m  3651.09h  152.13d  0.417 y
# IO & Wait Time:                 68503s    1141.71m    19.03h    0.79d  0.002 y
# Average job time:                 461s       7.68m     0.13h    0.01d
# Longest finished job:           10393s     173.22m     2.89h    0.12d
# Submission to last job:         54285s     904.75m    15.08h    0.63d

    cat offTargets/run.time | sed -e 's/^/# /;'
# Completed: 155244 of 155244 jobs
# CPU time in finished jobs:    2205628s   36760.46m   612.67h   25.53d  0.070 y
# IO & Wait Time:                825117s   13751.95m   229.20h    9.55d  0.026 y
# Average job time:                  20s       0.33m     0.01h    0.00d
# Longest finished job:             157s       2.62m     0.04h    0.00d
# Submission to last job:          5940s      99.00m     1.65h    0.07d

    # cleaning 2021-04-24 - Hiram
    time (~/kent/src/hg/utils/automation/doCrispr.pl -verbose=2 \
       -continue=cleanup panPan3 -tableName=crisprAll -fileServer=hgwdev \
    -buildDir=`pwd` -smallClusterHub=hgwdev -bigClusterHub=ku \
      -workhorse=hgwdev) > cleanup.log 2>&1
    # real    473m37.404s

#########################################################################
# all.joiner update, downloads and in pushQ - (WORKING - 2020-06-15 - Hiram)
    cd $HOME/kent/src/hg/makeDb/schema
    # verify all the business is done for release
    ~/kent/src/hg/utils/automation/verifyBrowser.pl panPan3
# 64 tables in database panPan3 - Bonobo, Pan paniscus
# verified 62 tables in database panPan3, 2 extra tables, 24 optional tables
# NCBI RefSeq genes     10 optional tables
# chainNetRBestHg38     3 optional tables
# chainNetRBestMm10     3 optional tables
# chainNetSynHg38       3 optional tables
# chainNetSynMm10       3 optional tables
# gapOverlap    1 optional tables
# tandemDups    1 optional tables
# 1     crisprAllRanges - extra table
# 2     crisprAllTargets        - extra table
# 9 genbank tables found
# verified 29 required tables, 0 missing tables
# hg38 chainNet to panPan3 found 3 required tables
# mm10 chainNet to panPan3 found 3 required tables
# hg38 chainNet RBest and syntenic to panPan3 found 6 optional tables
# mm10 chainNet RBest and syntenic to panPan3 found 3 optional tables
# liftOver to previous versions: 2, from previous versions: 2

    # fixup all.joiner until this is a clean output
    joinerCheck -database=panPan3 -tableCoverage all.joiner
    joinerCheck -database=panPan3 -times all.joiner
    joinerCheck -database=panPan3 -keys all.joiner

    # when clean, check in:
    git commit -m 'adding rules for panPan3 refs #25720' all.joiner
    git push
    # run up a 'make alpha' in hg/hgTables to get this all.joiner file
    # into the hgwdev/genome-test system

    cd /hive/data/genomes/panPan3
    time (~/kent/src/hg/utils/automation/makeDownloads.pl panPan3) > downloads.log 2>&1
    #  real    17m56.213s

    #   now ready for pushQ entry
    mkdir /hive/data/genomes/panPan3/pushQ
    cd /hive/data/genomes/panPan3/pushQ
 time ($HOME/kent/src/hg/utils/automation/makePushQSql.pl -redmineList panPan3) > panPan3.pushQ.sql 2> stderr.out
    # real    13m55.634s

    # remove the tandemDups and gapOverlap from the file list:
    sed -i -e "/tandemDups/d" redmine.panPan3.table.list
    sed -i -e "/Tandem Dups/d" redmine.panPan3.releaseLog.txt
    sed -i -e "/gapOverlap/d" redmine.panPan3.table.list
    sed -i -e "/Gap Overlaps/d" redmine.panPan3.releaseLog.txt

    #   check for errors in stderr.out, some are OK, e.g.:
    # WARNING: panPan3 does not have seq
    # WARNING: panPan3 does not have extFile

    # verify the file list does correctly match to files
    cat redmine.panPan3.file.list | while read L
do
  eval ls $L > /dev/null
done
    # should be silent, missing files will show as errors

    # verify database tables, how many to expect:
    wc -l redmine.panPan3.table.list
    # 53 redmine.panPan3.table.list

    # how many actual:
    awk -F'.' '{printf "hgsql -N %s -e '"'"'show table status like \"%s\";'"'"'\n", $1, $2}' redmine.panPan3.table.list | sh | wc -l
    # 53

    # would be a smaller number actual if some were missing

    # add the path names to the listing files in the redmine issue
    # in the three appropriate entry boxes:

#	/hive/data/genomes/panPan3/pushQ/redmine.panPan3.file.list
#	/hive/data/genomes/panPan3/pushQ/redmine.panPan3.releaseLog.txt
#	/hive/data/genomes/panPan3/pushQ/redmine.panPan3.table.list

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