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

# This file describes browser build for the dipOrd2

#########################################################################
# reuse photograph obtained for dipOrd1 previous versions
#    (DONE - 2017-12-22 - Hiram)

mkdir /hive/data/genomes/dipOrd2
cd /hive/data/genomes/dipOrd2
cp -p ../dipOrd1/photoReference.txt .

photoCreditURL  http://en.wikipedia.org/wiki/File:Kangaroo-rat.jpg
photoCreditName US Fish & Wildlife

#########################################################################
#  Initial steps (DONE - 2017-12-22 - Hiram)

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

mkdir ~/kent/src/hg/makeDb/doc/dipOrd2
cd ~/kent/src/hg/makeDb/doc/dipOrd2

# best to use a most recent document since it has the latest features and
# procedures:
sed -e 's/xenTro9/dipOrd2/g; s/XenTro9/DipOrd2/g; s/TBD/TBD/g;' \
    ../xenTro9/initialBuild.txt > initialBuild.txt

mkdir /hive/data/genomes/dipOrd2/refseq
cd /hive/data/genomes/dipOrd2/refseq

time rsync -L -a -P \
rsync://ftp.ncbi.nlm.nih.gov/genomes/refseq/vertebrate_mammalian/Dipodomys_ordii/all_assembly_versions/GCF_000151885.1_Dord_2.0/ ./

# sent 527 bytes  received 2353529223 bytes  16632719.08 bytes/sec
# total size is 2353239289  speedup is 1.00
# real    2m20.622s

# check assembly size for later reference:

faSize G*0_genomic.fna.gz
# 2236368823 bases (171054779 N's 2065314044 real 1260901403 upper
#	804412641 lower) in 65193 sequences in 1 files
# Total size: mean 34303.8 sd 716613.2 min 200 (NW_012315564.1)
#	max 68039765 (NW_012267217.1) median 2275
# %35.97 masked total, %38.95 masked real

# this information is from the top of 
#    dipOrd2/refseq/GCF_000151885.1_Dord_2.0_assembly_report.txt

# Assembly name:  Dord_2.0
# Organism name:  Dipodomys ordii (Ord's kangaroo rat)
# Isolate:  6190
# Sex:  female
# Taxid:          10020
# BioSample:      SAMN02900551
# BioProject:     PRJNA20385
# Submitter:      Baylor College of Medicine
# Date:           2014-12-12
# Assembly type:  haploid
# Release type:   major
# Assembly level: Scaffold
# Genome representation: full
# WGS project:    ABRO02
# Assembly method: AllPaths LG v. 41070; Atlas Link v. 2.0; Atlas GapFill v. 2.0
# Expected final version: yes
# Reference guided assembly: de-novo
# Genome coverage: 181.0x Illumina; 2.5x Sanger
# Sequencing technology: Illumina; Sanger dideoxy sequencing
# RefSeq category: Representative Genome
# GenBank assembly accession: GCA_000151885.2
# RefSeq assembly accession: GCF_000151885.1
# RefSeq assembly and GenBank assemblies identical: yes
#
## Assembly-Units:
## GenBank Unit Accession       RefSeq Unit Accession   Assembly-Unit name
## GCA_000151895.2      GCF_000151895.1 Primary Assembly

#############################################################################
# establish config.ra file (DONE - Hiram - 2017-12-22)
    # arguments here are: <db> <clade> <trackDbDir> <assembly_report.txt>
    cd /hive/data/genomes/dipOrd2
    $HOME/kent/src/hg/utils/automation/prepConfig.pl dipOrd2 mammal \
         kangarooRat ./refseq/*_assembly_report.txt > dipOrd2.config.ra

    # fixup common name to remain compatible with previous dipOrd1 versions:
    # commonName Ord's kangaroo rat
    # change to
    # commonName Kangaroo rat
    # and orderKey wasn't correct since it is based on the commonName
    # there is no chrM sequence, set
    # mitoAcc none

    # verify it looks sane
    cat dipOrd2.config.ra
# config parameters for makeGenomeDb.pl:
db dipOrd2
clade mammal
genomeCladePriority 35
scientificName Dipodomys ordii
commonName Kangaroo rat
assemblyDate Dec. 2014
assemblyLabel Baylor College of Medicine
assemblyShortLabel Dord_2.0
orderKey 11009
mitoAcc none
fastaFiles /hive/data/genomes/dipOrd2/ucsc/*.fa.gz
agpFiles /hive/data/genomes/dipOrd2/ucsc/*.agp
# qualFiles none
dbDbSpeciesDir kangarooRat
photoCreditURL  http://en.wikipedia.org/wiki/File:Kangaroo-rat.jpg
photoCreditName US Fish & Wildlife
ncbiGenomeId 772
ncbiAssemblyId 234081
ncbiAssemblyName Dord_2.0
ncbiBioProject 20385
ncbiBioSample SAMN02900551
genBankAccessionID GCF_000151885.1
taxId 10020

#############################################################################
# setup UCSC named files (DONE - 2017-12-22 - Hiram)

    mkdir /hive/data/genomes/dipOrd2/ucsc
    cd /hive/data/genomes/dipOrd2/ucsc

    # check for duplicate sequences:
    time faToTwoBit -noMask ../refseq/G*0_assembly_structure/Primary_Assembly/unplaced_scaffolds/FASTA/unplaced.scaf.fna.gz refseq.2bit
    #  real    0m51.705s

    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

    # simple assembly of unplaced contigs, change the .1 names to v1:
    zcat ../refseq/G*0_assembly_structure/Primary_Assembly/unplaced_scaffolds/FASTA/unplaced.scaf.fna.gz  \
	| sed -e 's/\.1 Dipo.*/v1/;' | gzip -c > chrUn.fa.gz
    zcat ../refseq/G*0_assembly_structure/Primary_Assembly/unplaced_scaffolds/AGP/unplaced.scaf.agp.gz  \
	| sed -e 's/\.1\t/v1\t/;' > chrUn.agp

    # verify fasta and AGPs agree
    time faToTwoBit chr*.fa.gz test.2bit
    # real    0m54.702s

    time cat chr*.agp | checkAgpAndFa stdin test.2bit 2>&1 | tail -4
    # All AGP and FASTA entries agree - both files are valid
    # real    0m45.356s

    # and no sequence lost from orginal:
    twoBitToFa test.2bit stdout | faSize stdin
# 2236368823 bases (171054779 N's 2065314044 real 2065314044 upper 0 lower)
#	in 65193 sequences in 1 files
# Total size: mean 34303.8 sd 716613.2 min 200 (NW_012315564v1)
#	max 68039765 (NW_012267217v1) median 2275

    # same numbers as above
# 2236368823 bases (171054779 N's 2065314044 real 1260901403 upper
#	804412641 lower) in 65193 sequences in 1 files
# Total size: mean 34303.8 sd 716613.2 min 200 (NW_012315564.1)
#	max 68039765 (NW_012267217.1) median 2275

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

#############################################################################
#  Initial database build (DONE - 2017-12-22 - Hiram)

    cd /hive/data/genomes/dipOrd2
    # verify sequence and AGP are OK:
    time (makeGenomeDb.pl -workhorse=hgwdev -dbHost=hgwdev -fileServer=hgwdev \
         -stop=agp dipOrd2.config.ra) > agp.log 2>&1
    # real    2m32.090s

    # then finish it off:
    time (makeGenomeDb.pl -workhorse=hgwdev -dbHost=hgwdev \
       -fileServer=hgwdev -continue=db dipOrd2.config.ra) > db.log 2>&1
    # real    16m55.183s

    # check in the trackDb files created in TemporaryTrackDbCheckout/
    #    and add dipOrd2 to trackDb/makefile

    # temporary symlink until masked sequence is available
    cd /hive/data/genomes/dipOrd2
    ln -s `pwd`/dipOrd2.unmasked.2bit /gbdb/dipOrd2/dipOrd2.2bit

##############################################################################
# cpgIslands on UNMASKED sequence (DONE - 2017-12-22 - Hiram)
    mkdir /hive/data/genomes/dipOrd2/bed/cpgIslandsUnmasked
    cd /hive/data/genomes/dipOrd2/bed/cpgIslandsUnmasked

    time (doCpgIslands.pl -dbHost=hgwdev -bigClusterHub=ku -buildDir=`pwd` \
       -tableName=cpgIslandExtUnmasked \
          -maskedSeq=/hive/data/genomes/dipOrd2/dipOrd2.unmasked.2bit \
             -workhorse=hgwdev -smallClusterHub=ku dipOrd2) > do.log 2>&1
    # real    7m12.778s

    cat fb.dipOrd2.cpgIslandExtUnmasked.txt
    # 79664500 bases of 2065314047 (3.857%) in intersection

#############################################################################
# cytoBandIdeo - (DONE - 2017-12-22 - Hiram)
    mkdir /hive/data/genomes/dipOrd2/bed/cytoBand
    cd /hive/data/genomes/dipOrd2/bed/cytoBand
    makeCytoBandIdeo.csh dipOrd2

##########################################################################
# run up idKeys files for chromAlias (DONE - 2017-12-22 - Hiram)
    mkdir /hive/data/genomes/dipOrd2/bed/idKeys
    cd /hive/data/genomes/dipOrd2/bed/idKeys

    time (doIdKeys.pl -twoBit=/hive/data/genomes/dipOrd2/dipOrd2.unmasked.2bit -buildDir=`pwd`  dipOrd2) > do.log 2>&1 &
    # real    12m20.939s

    cat dipOrd2.keySignature.txt
    #   8ae219619932349bebc17364408bf9d0

##########################################################################
# ucscToINSDC and ucscToRefSeq table/track (DONE - 2017-12-22 - Hiram)
    # the sequence here is working for a 'refseq' assembly
    # beware of a chrM situation may be specific depending upon what is
    # available in the assembly

    mkdir /hive/data/genomes/dipOrd2/bed/ucscToINSDC
    cd /hive/data/genomes/dipOrd2/bed/ucscToINSDC

    # there is no chrM sequence in this assembly

    # if there is a chrM, use its INSDC name as a second argument:
    # this is a RefSeq assembly, use the chrM refSeq name:
    ~/kent/src/hg/utils/automation/ucscToINSDC.sh \
      ../../refseq/GCF_*structure/Primary_Assembly

    # this is actually ucscToRefSeq since this is a RefSeq assembly
    sort -k2 ucscToINSDC.txt > ucscToRefSeq.txt

    rm -f ucscToINSDC.txt
    # there is also a genbank release, need to make idKeys to match it
    mkdir /hive/data/genomes/dipOrd2/bed/ucscToINSDC/genbank
    cd /hive/data/genomes/dipOrd2/bed/ucscToINSDC/genbank
    ln -s ../../../genbank/*ure/Pri*/unplaced_scaffolds/FASTA/*.fna.gz .
    faToTwoBit unplaced.scaf.fna.gz genbank.dipOrd2.2bit

    time (doIdKeys.pl -buildDir=`pwd` \
	-twoBit=`pwd`/genbank.dipOrd2.2bit genbankDipOrd2) > do.log 2>&1 &
    # real    30m4.448s

    cd /hive/data/genomes/dipOrd2/bed/ucscToINSDC
    join -t$'\t' \
      ../idKeys/dipOrd2.idKeys.txt genbank/genbankDipOrd2.idKeys.txt \
	| cut -f2- | sort > ucscToINSDC.txt

    awk '{printf "%s\t%s\n", $2, $1}' ucscToRefSeq.txt \
       | sort > refSeqToUcsc.txt

    awk '{printf "%s\t0\t%d\n", $1,$2}' ../../chrom.sizes \
         | sort > ucsc.coordinate.tab

    join -t$'\t' ucsc.coordinate.tab ucscToRefSeq.txt > ucscToRefSeq.bed
    join -t$'\t' ucsc.coordinate.tab ucscToINSDC.txt > ucscToINSDC.bed

    # should be same line counts throughout:
    # in this case one is missing in the final result due to the duplicate
    # contig being removed
    wc -l *
    # 65193 ucsc.coordinate.tab
    # 65193 ucscToINSDC.bed
    # 65193 ucscToINSDC.txt
    # 65193 ucscToRefSeq.bed
    # 65193 ucscToRefSeq.txt

    export chrSize=`cut -f1 ucscToINSDC.bed | awk '{print length($0)}' | sort -n | tail -1`
    echo $chrSize
    # 14
    # use the 14 in this sed
    sed -e "s/21/$chrSize/" $HOME/kent/src/hg/lib/ucscToINSDC.sql \
         | hgLoadSqlTab dipOrd2 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 $chrSize
    #  14
    sed -e "s/21/$chrSize/" $HOME/kent/src/hg/lib/ucscToINSDC.sql \
       | sed -e 's/INSDC/RefSeq/g;' > ucscToRefSeq.sql
    hgLoadSqlTab dipOrd2 ucscToRefSeq ./ucscToRefSeq.sql ucscToRefSeq.bed

    # checkTableCoords should be silent
    checkTableCoords dipOrd2
    # each should cover %100 entirely:
    featureBits -countGaps dipOrd2 ucscToINSDC
    # 2236368823 bases of 2236368823 (100.000%) in intersection

    featureBits -countGaps dipOrd2 ucscToRefSeq
    # 2236368823 bases of 2236368823 (100.000%) in intersection

#########################################################################
# add chromAlias table (DONE - 2017-12-22 - Hiram)

    mkdir /hive/data/genomes/dipOrd2/bed/chromAlias
    cd /hive/data/genomes/dipOrd2/bed/chromAlias

    # after ensembl idKeys have been made:
    join -t$'\t'  ../idKeys/dipOrd2.idKeys.txt \
	../../ensembl/ensemblDipOrd2.idKeys.txt | cut -f2- > ucsc.ensembl.tab

    hgsql -N -e 'select chrom,name from ucscToRefSeq;' dipOrd2 \
        > ucsc.refseq.tab
    hgsql -N -e 'select chrom,name from ucscToINSDC;' dipOrd2 \
        > ucsc.genbank.tab

    ~/kent/src/hg/utils/automation/chromAlias.pl ucsc.*.tab \
	> dipOrd2.chromAlias.tab

for t in refseq genbank ensembl
do
  c0=`cat ucsc.$t.tab | wc -l`
  c1=`grep $t dipOrd2.chromAlias.tab | wc -l`
  ok="OK"
  if [ "$c0" -ne "$c1" ]; then
     ok="ERROR"
  fi
  printf "# checking $t: $c0 =? $c1 $ok\n"
done
# checking refseq: 65193 =? 65193 OK
# checking genbank: 65193 =? 65193 OK
# checking ensembl: 65193 =? 65193 OK

    hgLoadSqlTab dipOrd2 chromAlias ~/kent/src/hg/lib/chromAlias.sql \
        dipOrd2.chromAlias.tab

#########################################################################
# fixup search rule for assembly track/gold table (DONE - 2017-12-22 - Hiram)
    cd ~/kent/src/hg/makeDb/trackDb/kangarooRat/dipOrd2

    # preview prefixes and suffixes:
    hgsql -N -e "select frag from gold;" dipOrd2 \
      | sed -e 's/[0-9][0-9]*//;' | sort | uniq -c 
#   148226 ABRO.1

    # implies a rule: 'ABRO[0-9]+(\.[0-9]+)?'

    # verify this rule will find them all and eliminate them all:
    hgsql -N -e "select frag from gold;" dipOrd2 | wc -l
    # 148226

    hgsql -N -e "select frag from gold;" dipOrd2 \
       | egrep -e 'ABRO[0-9]+(\.[0-9]+)?' | wc -l
    # 148226

    hgsql -N -e "select frag from gold;" dipOrd2 \
       | egrep -v -e 'ABRO[0-9]+(\.[0-9]+)?' | wc -l
    # 0

    # hence, add to trackDb/chicken/dipOrd2/trackDb.ra
searchTable gold
shortCircuit 1
termRegex ABRO[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 for these name patterns

##########################################################################
# running repeat masker (DONE - 2017-12-22 - Hiram)
    mkdir /hive/data/genomes/dipOrd2/bed/repeatMasker
    cd /hive/data/genomes/dipOrd2/bed/repeatMasker
    time  (doRepeatMasker.pl -buildDir=`pwd` \
        -bigClusterHub=ku -dbHost=hgwdev -workhorse=hgwdev \
        -smallClusterHub=ku dipOrd2) > do.log 2>&1 &
    # real    462m52.098s
    # XXX 8 jobs could not finish, cross_match does not complete
    # they were broken up into 50,000 base chunks and run separately
    # the results were placed into RMPart/005/000/
# -rw-rw-r-- 1  1095629 Dec 30 21:21 lift8bits.fa.out
# -rw-rw-r-- 1 10233429 Dec 30 21:21 lift8bits.fa.align

    # see if cat step will work correctly
    time  (doRepeatMasker.pl -buildDir=`pwd` \
        -bigClusterHub=ku -dbHost=hgwdev -workhorse=hgwdev \
        -continue=cat -stop=cat -smallClusterHub=ku dipOrd2) > cat.log 2>&1
    # real    9m20.559s

    # seems to be OK, continuing:
    time  (doRepeatMasker.pl -buildDir=`pwd` \
        -bigClusterHub=ku -dbHost=hgwdev -workhorse=hgwdev \
        -continue=mask -smallClusterHub=ku dipOrd2) > mask.log 2>&1
    # real    14m37.290s


    cat faSize.rmsk.txt
# 2236368823 bases (171054779 N's 2065314044 real 1321230680 upper
#	744083364 lower) in 65193 sequences in 1 files
# Total size: mean 34303.8 sd 716613.2 min 200 (NW_012315564v1)
#	max 68039765 (NW_012267217v1) median 2275
# %33.27 masked total, %36.03 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 dipOrd2 rmsk
    # 744619771 bases of 2236368823 (33.296%) in intersection
    # real    0m47.760s

    # 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;' dipOrd2 \
        | bedSingleCover.pl stdin | ave -col=4 stdin | grep "^total"
    #	total 744619771.000000
    #   real    0m33.003s

##########################################################################
# running simple repeat (DONE - 2017-12-22 - Hiram)

    mkdir /hive/data/genomes/dipOrd2/bed/simpleRepeat
    cd /hive/data/genomes/dipOrd2/bed/simpleRepeat
    # using trf409 5 here a bit smaller genome (human == 6)
    time (doSimpleRepeat.pl -buildDir=`pwd` -bigClusterHub=ku \
        -dbHost=hgwdev -workhorse=hgwdev -smallClusterHub=ku \
        -trf409 5 dipOrd2) > do.log 2>&1 &
    # real    394m21.273s

    cat fb.simpleRepeat
    # 170021835 bases of 2065314047 (8.232%) in intersection

    # adding this trfMask to the other masking
    cd /hive/data/genomes/dipOrd2

    # when using the Window Masker result:
#    twoBitMask bed/windowMasker/dipOrd2.cleanWMSdust.2bit \
#       -add bed/simpleRepeat/trfMask.bed  dipOrd2.2bit
    #   you can safely ignore the warning about fields >= 13

    # when using Rmsk results, add to rmsk after it is done:
    twoBitMask dipOrd2.rmsk.2bit \
        -add bed/simpleRepeat/trfMask.bed dipOrd2.2bit
    #   you can safely ignore the warning about fields >= 13

    twoBitToFa dipOrd2.2bit stdout | faSize stdin > faSize.dipOrd2.2bit.txt
    cat faSize.dipOrd2.2bit.txt
# 2236368823 bases (171054779 N's 2065314044 real 1290537444 upper
#	774776600 lower) in 65193 sequences in 1 files
# Total size: mean 34303.8 sd 716613.2 min 200 (NW_012315564v1)
#	max 68039765 (NW_012267217v1) median 2275
# %34.64 masked total, %37.51 masked real

    # reset the symlink
    rm /gbdb/dipOrd2/dipOrd2.2bit
    ln -s `pwd`/dipOrd2.2bit /gbdb/dipOrd2/dipOrd2.2bit

#########################################################################
# CREATE MICROSAT TRACK (DONE - 2017-12-30 - Hiram)
    ssh hgwdev
    mkdir /cluster/data/dipOrd2/bed/microsat
    cd /cluster/data/dipOrd2/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 dipOrd2 microsat microsat.bed
    # Read 104987 elements of size 4 from microsat.bed

##########################################################################
## WINDOWMASKER (DONE - 2017-12-30 - Hiram)

    mkdir /hive/data/genomes/dipOrd2/bed/windowMasker
    cd /hive/data/genomes/dipOrd2/bed/windowMasker
    time (doWindowMasker.pl -buildDir=`pwd` -workhorse=hgwdev \
        -dbHost=hgwdev dipOrd2) > do.log 2>&1
    # real    199m45.928s

    # Masking statistics
    cat faSize.dipOrd2.cleanWMSdust.txt
# 2236368823 bases (171054779 N's 2065314044 real 1246991941 upper
#	818322103 lower) in 65193 sequences in 1 files
# Total size: mean 34303.8 sd 716613.2 min 200 (NW_012315564v1)
#	max 68039765 (NW_012267217v1) median 2275
# %36.59 masked total, %39.62 masked real


    cat fb.dipOrd2.rmsk.windowmaskerSdust.txt
    # 542455834 bases of 2236368823 (24.256%) in intersection

##########################################################################
# cpgIslands - (DONE - 2017-12-31 - Hiram)
    mkdir /hive/data/genomes/dipOrd2/bed/cpgIslands
    cd /hive/data/genomes/dipOrd2/bed/cpgIslands
    time (doCpgIslands.pl -dbHost=hgwdev -bigClusterHub=ku \
      -workhorse=hgwdev -smallClusterHub=ku dipOrd2) > do.log 2>&1 &
    # real    7m7.765s

    cat fb.dipOrd2.cpgIslandExt.txt
    # 20939057 bases of 2065314047 (1.014%) in intersection

##############################################################################
# genscan - (DONE - 2017-12-31 - Hiram)
    mkdir /hive/data/genomes/dipOrd2/bed/genscan
    cd /hive/data/genomes/dipOrd2/bed/genscan
    time (doGenscan.pl -buildDir=`pwd` -workhorse=hgwdev -dbHost=hgwdev \
      -bigClusterHub=ku dipOrd2) > do.log 2>&1 &
    # real    395m13.441s

    cat fb.dipOrd2.genscan.txt
    # 50439107 bases of 2065314047 (2.442%) in intersection

    cat fb.dipOrd2.genscanSubopt.txt
    # 44013285 bases of 2065314047 (2.131%) in intersection

#############################################################################
# augustus gene track (DONE - 2017-12-31 - Hiram)

    mkdir /hive/data/genomes/dipOrd2/bed/augustus
    cd /hive/data/genomes/dipOrd2/bed/augustus

    time (doAugustus.pl -buildDir=`pwd` -bigClusterHub=ku \
     -species=human -dbHost=hgwdev -workhorse=hgwdev dipOrd2) > do.log 2>&1 &
    # real    162m42.872s

    cat fb.dipOrd2.augustusGene.txt
    # 44381136 bases of 2065314047 (2.149%) in intersection

    featureBits -enrichment dipOrd2 augustusGene ensGene
# augustusGene 2.149%, ensGene 1.670%, both 1.212%, cover 56.42%, enrich 33.77x

#############################################################################
# lastz/chain/net swap human/hg38 (DONE - 2018-01-02 - Hiram)
    # original alignment
    cd /hive/data/genomes/hg38/bed/lastzDipOrd2.2018-01-01

    cat fb.hg38.chainDipOrd2Link.txt
    # 1001007354 bases of 3049335806 (32.827%) in intersection
    cat fb.hg38.chainSynDipOrd2Link.txt
    # 934602735 bases of 3049335806 (30.649%) in intersection
    cat fb.hg38.chainRBestDipOrd2Link.txt
    # 921538020 bases of 3049335806 (30.221%) in intersection

    # and for the swap:
    mkdir /hive/data/genomes/dipOrd2/bed/blastz.hg38.swap
    cd /hive/data/genomes/dipOrd2/bed/blastz.hg38.swap
    time (doBlastzChainNet.pl -verbose=2 \
        /hive/data/genomes/hg38/bed/lastzDipOrd2.2018-01-01/DEF \
        -chainMinScore=3000 -chainLinearGap=medium \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -swap -syntenicNet) > swap.log 2>&1 &
    # real    97m8.750s

    cat fb.dipOrd2.chainHg38Link.txt
    # 957281496 bases of 2065314047 (46.350%) in intersection
    cat fb.dipOrd2.chainSynHg38Link.txt
    # 905805640 bases of 2065314047 (43.858%) in intersection

    time (doRecipBest.pl -load -workhorse=hgwdev \
	-buildDir=`pwd` dipOrd2 hg38) > rbest.log 2>&1 &
    # real    431m28.226s

    cat fb.dipOrd2.chainRBestHg38Link.txt
    # 923041001 bases of 2065314047 (44.693%) in intersection

##############################################################################
# lastz/chain/net swap mouse/mm10 (DONE - 2018-01-02 - Hiram)
    # original alignment to mm10
    cd /hive/data/genomes/mm10/bed/lastzDipOrd2.2018-01-01

    cat fb.mm10.chainDipOrd2Link.txt
    #	645178768 bases of 2652783500 (24.321%) in intersection
    cat fb.mm10.chainRBestDipOrd2Link.txt
    # 605074450 bases of 2652783500 (22.809%) in intersection

    mkdir /hive/data/genomes/dipOrd2/bed/blastz.mm10.swap
    cd /hive/data/genomes/dipOrd2/bed/blastz.mm10.swap
    time (doBlastzChainNet.pl -verbose=2 \
	/hive/data/genomes/mm10/bed/lastzDipOrd2.2018-01-01/DEF \
	-swap -syntenicNet \
	-workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
	-chainMinScore=3000 -chainLinearGap=medium) > swap.log 2>&1
    #	real    79m46.564s

    cat fb.dipOrd2.chainMm10Link.txt
    # 631879699 bases of 2065314047 (30.595%) in intersection
    cat fb.dipOrd2.chainSynMm10Link.txt
    # 581661824 bases of 2065314047 (28.163%) in intersection


    time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` dipOrd2 mm10) \
	> rbest.log 2>&1
    # real    412m53.879s

    cat fb.dipOrd2.chainRBestMm10Link.txt
    # 605056621 bases of 2065314047 (29.296%) in intersection

##############################################################################
# Create kluster run files (DONE - 2017-12-31 - Hiram)

    # numerator is dipOrd2 gapless bases "real" as reported by:
    featureBits -noRandom -noHap dipOrd2 gap
    # 171054776 bases of 2065314047 (8.282%) 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 \( 2065314047 / 2861349177 \) \* 1024
    #  ( 2065314047 / 2861349177 ) * 1024 = 739.120413

    # ==> use -repMatch=750 according to size scaled down from 1024 for human.
    #   and rounded up to nearest 50
    cd /hive/data/genomes/dipOrd2
    blat dipOrd2.2bit \
         /dev/null /dev/null -tileSize=11 -makeOoc=jkStuff/dipOrd2.11.ooc \
        -repMatch=750
    #   Wrote 29353 overused 11-mers to jkStuff/dipOrd2.11.ooc
    # dipOrd1 was: -repMatch=700
    #	Wrote 33062 overused 11-mers to dipOrd1.11.ooc

    #   check non-bridged gaps to see what the typical size is:
    hgsql -N \
        -e 'select * from gap where bridge="no" order by size;' dipOrd2 \
        | sort -k7,7nr | ave -col=7 stdin
    # there are no non-bridged gaps in this assembly

    # # all these gap sizes are 100
    # # minimum gap size is 100 and produces a reasonable number of lifts
    # gapToLift -verbose=2 -minGap=10 dipOrd2 jkStuff/nonBridged.lft \
    #    -bedFile=jkStuff/nonBridged.bed

#########################################################################
# LIFTOVER TO dipOrd1 (DONE - 2017-12-31 - Hiram)
    ssh hgwdev
    mkdir /hive/data/genomes/dipOrd2/bed/blat.dipOrd1.2017-12-31
    cd /hive/data/genomes/dipOrd2/bed/blat.dipOrd1.2017-12-31
    time (doSameSpeciesLiftOver.pl -verbose=2 -buildDir=`pwd` \
	-ooc=/hive/data/genomes/dipOrd2/jkStuff/dipOrd2.11.ooc \
        -bigClusterHub=ku -dbHost=hgwdev -workhorse=hgwdev \
         dipOrd2 dipOrd1) > do.log 2>&1
    # real    1026m23.658s

    # verify the convert link on the test browser is now active from dipOrd2 to
    # dipOrd1

#########################################################################
# GENBANK AUTO UPDATE (DONE - 2017-12-31 - Hiram)
    ssh hgwdev
    cd $HOME/kent/src/hg/makeDb/genbank
    git pull
    # /cluster/data/genbank/data/organism.lst shows:
    # #organism             mrnaCnt   estCnt  refSeqCnt
    # Dipodomys merriami      5       0       0
    # Dipodomys spectabilis   7       0       0

    # there appear to be none for Dipodomys ordii

    # edit etc/genbank.conf to add dipOrd2 just before dipOrd1
# dipOrd2 (Kangaroo rat)
dipOrd2.serverGenome = /hive/data/genomes/dipOrd2/dipOrd2.2bit
dipOrd2.clusterGenome = /hive/data/genomes/dipOrd2/dipOrd2.2bit
dipOrd2.ooc = /hive/data/genomes/dipOrd2/jkStuff/dipOrd2.11.ooc
dipOrd2.lift = no
dipOrd2.refseq.mrna.native.pslCDnaFilter  = ${ordered.refseq.mrna.native.pslCDnaFilter}
dipOrd2.refseq.mrna.xeno.pslCDnaFilter    = ${ordered.refseq.mrna.xeno.pslCDnaFilter}
dipOrd2.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter}
dipOrd2.genbank.mrna.xeno.pslCDnaFilter   = ${ordered.genbank.mrna.xeno.pslCDnaFilter}
dipOrd2.genbank.est.native.pslCDnaFilter  = ${ordered.genbank.est.native.pslCDnaFilter}
# there are zero native mrna or est for dipOrd
dipOrd2.refseq.mrna.native.load = no
dipOrd2.refseq.mrna.xeno.load = yes
# DO NOT NEED genbank.mrna.xeno except for human, mouse
dipOrd2.genbank.mrna.xeno.load = yes
dipOrd2.genbank.est.native.load = no
dipOrd2.downloadDir = dipOrd2
dipOrd2.perChromTables = no

    git commit -m 'adding dipOrd2 Dipodomys ordii refs #20751' etc/genbank.conf
    git push
    # update /cluster/data/genbank/:
    make etc-update

    cd /cluster/data/genbank

    time ./bin/gbAlignStep -initial dipOrd2
    # logFile: var/build/logs/2017.12.31-08:55:07.dipOrd2.initalign.log
    #   real    1098m37.667s

    tail -2 var/build/logs/2017.12.31-08:55:07.dipOrd2.initalign.log
    #	hgwdev 2018.01.01-03:04:33 dipOrd2.initalign: Succeeded: dipOrd2
    #	hgwdev 2018.01.01-03:13:45 dipOrd2.initalign: finish

    #   To re-do, rm the dir first:
    #     /cluster/data/genbank/work/initial.dipOrd2

    # load database when finished
    ssh hgwdev
    cd /cluster/data/genbank
    time ./bin/gbDbLoadStep -drop -initialLoad dipOrd2
    # logFile: var/dbload/hgwdev/logs/2018.01.01-13:04:41.dipOrd2.dbload.log
    #  real    98m36.682s

    tail -1 var/dbload/hgwdev/logs/2018.01.01-13:04:41.dipOrd2.dbload.log
    #  hgwdev 2018.01.01-14:43:18 dipOrd2.dbload: finish

    # enable daily alignment and update of hgwdev
    cd ~/kent/src/hg/makeDb/genbank
    git pull
    # add dipOrd2 to:
    #   etc/align.dbs etc/hgwdev.dbs
    git add etc/align.dbs etc/hgwdev.dbs
    git commit -m 'adding dipOrd2 to the update alignments refs #19151' etc/align.dbs etc/hgwdev.dbs
    git push
    make etc-update

#############################################################################
#  BLATSERVERS ENTRY (DONE - 2018-01-03 - 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 ("dipOrd2", "blat1d", "17894", "1", "0"); \
	INSERT INTO blatServers (db, host, port, isTrans, canPcr) \
	VALUES ("dipOrd2", "blat1d", "17895", "0", "1");' \
	    hgcentraltest
    #	test it with some sequence

############################################################################
## reset default position to same protein location as hg38
##  found by blat (DONE - 2018-01-03 - Hiram)

    ssh hgwdev
    hgsql -e 'update dbDb set defaultPos="NW_012267222v1:6911344-7030779"
	where name="dipOrd2";' hgcentraltest

#########################################################################
# all.joiner update, downloads and in pushQ - (TBD - 2017-03-06 - Hiram)
    cd $HOME/kent/src/hg/makeDb/schema
    # fixup all.joiner until this is a clean output
    joinerCheck -database=dipOrd2 -tableCoverage all.joiner
    joinerCheck -database=dipOrd2 -times all.joiner
    joinerCheck -database=dipOrd2 -keys all.joiner

    cd /hive/data/genomes/dipOrd2
    time (makeDownloads.pl -workhorse=hgwdev dipOrd2) > downloads.log 2>&1
    #  real    19m11.136s

    #   now ready for pushQ entry
    mkdir /hive/data/genomes/dipOrd2/pushQ
    cd /hive/data/genomes/dipOrd2/pushQ
  time (makePushQSql.pl -redmineList dipOrd2) > dipOrd2.pushQ.sql 2> stderr.out
    #  real    3m55.668s

    #   check for errors in stderr.out, some are OK, e.g.:
    # WARNING: dipOrd2 does not have seq
    # WARNING: dipOrd2 does not have extFile
    # WARNING: dipOrd2 does not have estOrientInfo

    ## there are warnings about the RBest and Syn chainNet tables, which we
    ## are not interested in at this time.  They can be left out.

    # verify the file listings are valid, should be no output to stderr:
    cat redmine.dipOrd2.file.list \
        | while read L; do ls -ogL $L; done  > /dev/null

    # to verify the database.table list is correct, should be the same
    # line count for these two commands:
    wc -l redmine.dipOrd2.table.list
    # 70 redmine.dipOrd2.table.list
    awk -F'.' '{
printf "hgsql -N -e \"show table status like '"'"'%s'"'"';\" %s\n", $2, $1
}' redmine.dipOrd2.table.list | while read L; do eval $L; done | wc -l
    # 70

    # enter the path names to these files in the redmine issue to
    # make QA Ready:
    ls `pwd`/redmine*

/hive/data/genomes/dipOrd2/pushQ/redmine.dipOrd2.file.list
/hive/data/genomes/dipOrd2/pushQ/redmine.dipOrd2.releaseLog.txt
/hive/data/genomes/dipOrd2/pushQ/redmine.dipOrd2.table.list

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