97cc4f47f34fca7bebb8bc8733d54a57a8d98839
hiram
  Fri Dec 9 14:25:51 2022 -0800
liftOver canFam6 to canFam2 refs #30374

diff --git src/hg/makeDb/doc/canFam6/initialBuild.txt src/hg/makeDb/doc/canFam6/initialBuild.txt
index 2a3b381..1b54cd9 100644
--- src/hg/makeDb/doc/canFam6/initialBuild.txt
+++ src/hg/makeDb/doc/canFam6/initialBuild.txt
@@ -1,1314 +1,1339 @@
 # for emacs: -*- mode: sh; -*-
 
 # This file describes browser build for the canFam6
 #	GCF_000002285.5_Dog10K_Boxer_Tasha
 
 #  Can use existing photograph (otherwise find one before starting here)
 
 #########################################################################
 #  Initial steps, reuse existing photograph (DONE - 2021-05-10 - Hiram)
 
 # To start this initialBuild.txt document, from a previous assembly document:
 
 mkdir ~/kent/src/hg/makeDb/doc/canFam6
 cd ~/kent/src/hg/makeDb/doc/canFam6
 
 sed -e 's/Fam5/Fam6/g; s/DONE/TBD/g;' \
    ../canFam5/initialBuild.txt > initialBuild.txt
 
 cd /hive/data/genomes/canFam6
 
 # This is the same individual as canFam3
 
 cp -p ../canFam3/photoReference.txt .
 cat photoReference.txt
 
 ## download from NCBI
 mkdir /hive/data/genomes/canFam6/refseq
 cd /hive/data/genomes/canFam6/refseq
 
 time rsync -L -a -P --stats \
 rsync://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/002/285/GCF_000002285.5_Dog10K_Boxer_Tasha/ ./
 
 # sent 4,942 bytes  received 4,079,561,723 bytes  48,278,895.44 bytes/sec
 # total size is 4,078,547,567  speedup is 1.00
 
 # real    1m23.798s
 
 # this information is from the top of 
 #    canFam6/refseq/*_assembly_report.txt
 #  (aka: canFam6/refseq/GCF_000002285.5_Dog10K_Boxer_Tasha_assembly_report.txt)
 
 # Assembly name:  Dog10K_Boxer_Tasha
 # Organism name:  Canis lupus familiaris (dog)
 # Infraspecific name:  breed=boxer
 # Sex:  female
 # Taxid:          9615
 # BioSample:      SAMN02953603
 # BioProject:     PRJNA13179
 # Submitter:      Dog Genome Sequencing Consortium
 # Date:           2020-10-06
 # Assembly type:  haploid
 # Release type:   major
 # Assembly level: Chromosome
 # Genome representation: full
 # WGS project:    AAEX04
 # Assembly method: Canu v. 1.8
 # Expected final version: yes
 # Genome coverage: 100.0x
 # Sequencing technology: PacBio Sequel
 # RefSeq category: Representative Genome
 # GenBank assembly accession: GCA_000002285.4
 # RefSeq assembly accession: GCF_000002285.5
 # RefSeq assembly and GenBank assemblies identical: no
 #
 ## Assembly-Units:
 ## GenBank Unit Accession       RefSeq Unit Accession   Assembly-Unit name
 ## GCA_000000145.4      GCF_000000145.4 Primary Assembly
 ## GCA_013123455.1      GCF_000184225.1 non-nuclear
 
 # check assembly size for later reference:
 
 time faSize G*a_genomic.fna.gz
 
 # 2312802198 bases (58852 N's 2312743346 real 1566802244 upper
 #	745941102 lower) in 147 sequences in 1 files
 # Total size: mean 15733348.3 sd 28607349.9 min 551 (NW_023329752.1)
 #	max 122014068 (NC_006583.4) median 7637
 # %32.25 masked total, %32.25 masked real
 
 # real    0m31.588s
 
 # Survey types of gaps:
 
 zgrep -v "^#" *gaps.txt.gz | cut -f5,6 | sort | uniq -c
 #    1015 within_scaffold paired-ends
 
 # And total size in gaps:
 zcat *gaps.txt.gz | grep -v "^#" | awk '{print $3-$2+1}' | ave stdin \
   | sed -e 's/^/# /;'
 # Q1 25.000000
 # median 25.000000
 # Q3 100.000000
 # average 57.969458
 # min 10.000000
 # max 100.000000
 # count 1015
 # total 58839.000000
 # standard deviation 37.178047
 
 #############################################################################
 # establish config.ra file (DONE - 2021-05-10 - Hiram)
     cd /hive/data/genomes/canFam6
     ~/kent/src/hg/utils/automation/prepConfig.pl canFam6 mammal dog \
        refseq/*_assembly_report.txt > canFam6.config.ra
 
     # compare with previous version to see if it is sane:
     diff canFam6.config.ra ../canFam3/canFam3.config.ra
 
     # verify it really does look sane
     cat canFam6.config.ra
 # config parameters for makeGenomeDb.pl:
 db canFam6
 clade mammal
 scientificName Canis lupus familiaris
 commonName Dog
 assemblyDate Oct. 2020
 assemblyLabel Dog Genome Sequencing Consortium
 assemblyShortLabel Dog10K_Boxer_Tasha
 orderKey 4660
 # mitochondrial sequence included in refseq release
 # mitoAcc NC_002008.4
 mitoAcc none
 fastaFiles /hive/data/genomes/canFam6/ucsc/*.fa.gz
 agpFiles /hive/data/genomes/canFam6/ucsc/*.agp
 # qualFiles none
 dbDbSpeciesDir dog
 photoCreditURL  http://www.genome.gov/dmd/img.cfm?node=Photos/Animals/Dog&id=79106
 photoCreditName NHGRI press photos
 ncbiGenomeId 85
 ncbiAssemblyId 8227741
 ncbiAssemblyName Dog10K_Boxer_Tasha
 ncbiBioProject 13179
 ncbiBioSample SAMN02953603
 genBankAccessionID GCF_000002285.5
 taxId 9615
 
 #############################################################################
 # setup UCSC named files (DONE - 2021-05-12 - Hiram)
 
     mkdir /hive/data/genomes/canFam6/ucsc
     cd /hive/data/genomes/canFam6/ucsc
 
     # check for duplicate sequences:
     time faToTwoBit -noMask ../refseq/G*a_genomic.fna.gz refseq.2bit
     #  real    0m32.374s
 
     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
 
     # compare gaps with what the gaps.gz file reported:
     twoBitInfo -nBed refseq.2bit  refseq.gap.bed
     awk '{print $3-$2}' *.gap.bed | ave stdin | sed -e 's/^/# /;'
 # Q1 25.000000
 # median 25.000000
 # Q3 100.000000
 # average 57.249027
 # min 1.000000
 # max 100.000000
 # count 1028
 # total 58852.000000
 # standard deviation 37.486982
 
     # comparing with above, there are 13 bases here that are not
     # counted in the NCBI gaps file.  See what the AGP says later on here.
 
     time ~/kent/src/hg/utils/automation/ucscCompositeAgp.pl \
       ../refseq/G*a_genomic.fna.gz \
 	../refseq/*_assembly_structure/Primary_Assembly
 NC_006583.4 chr1
 NC_006584.4 chr2
 NC_006585.4 chr3
 NC_006586.4 chr4
 NC_006587.4 chr5
 NC_006588.4 chr6
 NC_006589.4 chr7
 NC_006590.4 chr8
 NC_006591.4 chr9
 NC_006592.4 chr10
 NC_006593.4 chr11
 NC_006594.4 chr12
 NC_006595.4 chr13
 NC_006596.4 chr14
 NC_006597.4 chr15
 NC_006598.4 chr16
 NC_006599.4 chr17
 NC_006600.4 chr18
 NC_006601.4 chr19
 NC_006602.4 chr20
 NC_006603.4 chr21
 NC_006604.4 chr22
 NC_006605.4 chr23
 NC_006606.4 chr24
 NC_006607.4 chr25
 NC_006608.4 chr26
 NC_006609.4 chr27
 NC_006610.4 chr28
 NC_006611.4 chr29
 NC_006612.4 chr30
 NC_006613.4 chr31
 NC_006614.4 chr32
 NC_006615.4 chr33
 NC_006616.4 chr34
 NC_006617.4 chr35
 NC_006618.4 chr36
 NC_006619.4 chr37
 NC_006620.4 chr38
 NC_006621.4 chrX
 
 real    9m50.617s
 
     time ~/kent/src/hg/utils/automation/unplacedWithChroms.pl \
        ../refseq/*_assembly_structure/Primary_Assembly
     # processed 107 sequences into chrUn.fa.gz
 
     # real    0m1.551s
 
     # there are no unlocalized in this assembly
     time ~/kent/src/hg/utils/automation/unlocalizedWithChroms.pl \
        ../refseq/*_assembly_structure/Primary_Assembly
 
     # bash syntax here
     mitoAcc=`grep "^# mitoAcc" ../canFam6.config.ra | awk '{print $NF}'`
     printf "# mitoAcc %s\n" "$mitoAcc"
 # mitoAcc NC_002008.4
 
     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       16727   1       O       NC_002008.4     1       16727   +
 
     printf ">chrM\n" > chrM.fa
     twoBitToFa -noMask refseq.2bit:$mitoAcc stdout | grep -v "^>" >> chrM.fa
     gzip chrM.fa
 
     faSize chrM.fa.gz
 # 16727 bases (0 N's 16727 real 16727 upper 0 lower) in 1 sequences in 1 files
 
     # verify fasta and AGPs agree
     time faToTwoBit *.fa.gz test.2bit
     # real    0m44.947s
 
     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
 # 2312802198 bases (58852 N's 2312743346 real 2312743346 upper 0 lower)
 #	in 147 sequences in 1 files
 # Total size: mean 15733348.3 sd 28607349.9 min 551 (chrUn_NW_023329752v1)
 #	max 122014068 (chr1) median 7637
 
     # same numbers as above (except for upper/lower masking)
 # 2312802198 bases (58852 N's 2312743346 real 1566802244 upper
 #	745941102 lower) in 147 sequences in 1 files
 # Total size: mean 15733348.3 sd 28607349.9 min 551 (NW_023329752.1)
 #	max 122014068 (NC_006583.4) median 7637
 
     # Verify these AGP files define all the gaps:
     zgrep -w scaffold *.agp | awk '{print $3-$2+1}' | ave stdin
 # No numerical data column 1 of stdin
 
     # XXX It doesn't define any gaps at all, and they all the same:
     zgrep -v "^#" ../refseq/G*a_genomic_gaps.txt.gz \
           | awk '{print $5}' | sort | uniq -c
 #    1015 within_scaffold
 
     # Need to make up gaps with a fake AGP
     # Would like to use the 'component' identifier to make a fake AGP
     zgrep -h -v "^#" \
   ../refseq/G*ure/Primary_Assembly/assembled_chromosomes/AGP/*.comp.agp.gz \
        | awk -F$'\t' '{printf "s/%s/%s/;\n", $1, $6}' > ncbiComponent.sed
     zgrep -h -v "^#" \
   ../refseq/G*ure/Primary_Assembly/unplaced_scaffolds/AGP/unplaced.scaf.agp.gz \
        | awk -F$'\t' '{printf "s/%s/%s/;\n", $1, $6}' >> ncbiComponent.sed
 
     # using that sed file, convert the fasta names to component names
     # this works because there is only one component name per sequence,
     # wouldn't work if the AGP files were multiple lines
     twoBitToFa refseq.2bit stdout | sed -f ncbiComponent.sed \
        | hgFakeAgp -minContigGap=1 -minScaffoldGap=200000 -singleContigs \
           stdin fake.agp
 
     # convert those names back to UCSC chrom names
     zgrep -h -v "^#" chr*.agp | awk '{printf "s/%s/%s/;\n", $6,$1}' \
        | sort > ncbi.ucsc.sed 
     sed -f ncbi.ucsc.sed fake.agp > canFam6.fake.agp
 
     # should have only UCSC names in column 1
  cut -f1 canFam6.fake.agp | sort | uniq -c | sort -rn | head | sed -e 's/^/#/;'
 #    247 chr32
 #    193 chr34
 #    161 chr1
 #    157 chr6
 #    155 chr3
 #    119 chrX
 #     93 chr16
 #     75 chr37
 #     69 chr22
 #     55 chr11
  cut -f1 canFam6.fake.agp | sort | uniq -c | sort -rn | tail | sed -e 's/^/#/;'
 #      1 chrUn_NW_023329675v1
 #      1 chrUn_NW_023329674v1
 #      1 chrUn_NW_023329673v1
 #      1 chrUn_NW_023329672v1
 #      1 chrUn_NW_023329671v1
 #      1 chrUn_NW_023329670v1
 #      1 chrUn_NW_023329669v1
 #      1 chrUn_NW_023329668v1
 #      1 chrUn_NW_023329667v1
 #      1 chrM
 
 
     # verify this AGP file functions correctly:
     checkAgpAndFa canFam6.fake.agp test.2bit 2>&1 | tail -4
     
     # no longer need these temporary 2bit files
     rm test.2bit refseq.2bit refseq.2bit refseq.gap.bed fake.agp
 
     # Reset the AGP specification in canFam6.config.ra
 agpFiles /hive/data/genomes/canFam6/ucsc/canFam6.fake.agp
 
 #############################################################################
 #  Initial database build (DONE - 2021-05-12 - Hiram)
 
     # verify sequence and AGP are OK:
     cd /hive/data/genomes/canFam6
     time (makeGenomeDb.pl -workhorse=hgwdev -dbHost=hgwdev -fileServer=hgwdev \
          -stop=agp canFam6.config.ra) > agp.log 2>&1
     # real    1m56.533s
 
     # then finish it off:
     time (makeGenomeDb.pl -workhorse=hgwdev -dbHost=hgwdev \
        -fileServer=hgwdev -continue=db canFam6.config.ra) > db.log 2>&1
     # real    12m7.732s
 
     # check in the trackDb files created in TemporaryTrackDbCheckout/
     #    and add canFam6 to trackDb/makefile   refs #27546
     # fixing up the images reference to canFam6.jpg
 
     # temporary symlink until masked sequence is available
     cd /hive/data/genomes/canFam6
     ln -s `pwd`/canFam6.unmasked.2bit /gbdb/canFam6/canFam6.2bit
 
 #############################################################################
 # verify gap table vs NCBI gap file (DONE - 2021-05-12 - Hiram)
     mkdir /hive/data/genomes/canFam6/bed/gap
     cd /hive/data/genomes/canFam6/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
 #   1015 within_scaffold_paired-ends
 
     # how much defined by NCBI:
     awk '{print $3-$2}' *.bed | ave stdin | grep -w total
     # total 58839.000000
 
     # how much in the gap table:
     hgsql -e 'select * from gap;' canFam6 | awk '{print $4-$3}' \
 	| ave stdin | grep -w total
     # total 58852.000000
 
     # an extra 13 marked in the UCSC AGP file
 
 ##############################################################################
 # cpgIslands on UNMASKED sequence (DONE - 2021-05-12 - Hiram)
     mkdir /hive/data/genomes/canFam6/bed/cpgIslandsUnmasked
     cd /hive/data/genomes/canFam6/bed/cpgIslandsUnmasked
 
     time (doCpgIslands.pl -dbHost=hgwdev -bigClusterHub=ku -buildDir=`pwd` \
        -tableName=cpgIslandExtUnmasked \
           -maskedSeq=/hive/data/genomes/canFam6/canFam6.unmasked.2bit \
              -workhorse=hgwdev -smallClusterHub=ku canFam6) > do.log 2>&1
     # real    3m30.591s
 
     cat fb.canFam6.cpgIslandExtUnmasked.txt
     # 56535294 bases of 2481941580 (2.278%) in intersection
 
 #############################################################################
 # cytoBandIdeo - (DONE - 2021-05-12 - Hiram)
     mkdir /hive/data/genomes/canFam6/bed/cytoBand
     cd /hive/data/genomes/canFam6/bed/cytoBand
     makeCytoBandIdeo.csh canFam6
 
 #############################################################################
 # run up idKeys files for chromAlias/ncbiRefSeq (DONE - 2021-05-12 - Hiram)
     mkdir /hive/data/genomes/canFam6/bed/idKeys
     cd /hive/data/genomes/canFam6/bed/idKeys
 
     time (doIdKeys.pl \
         -twoBit=/hive/data/genomes/canFam6/canFam6.unmasked.2bit \
         -buildDir=`pwd` canFam6) > do.log 2>&1 &
     # real    0m32.977s
 
     cat canFam6.keySignature.txt
     #  efdede185d06fdca97de518811962150
 
 #############################################################################
 # gapOverlap (DONE - 2021-05-12 - Hiram)
     mkdir /hive/data/genomes/canFam6/bed/gapOverlap
     cd /hive/data/genomes/canFam6/bed/gapOverlap
     time (doGapOverlap.pl \
         -twoBit=/hive/data/genomes/canFam6/canFam6.unmasked.2bit canFam6 ) \
         > do.log 2>&1 &
     # real    19m39.531s
 
     # there are none, nothing to load
 
     # cat fb.canFam6.gapOverlap.txt
     # xxx bases of yyy (0.001%) in intersection
 
 #############################################################################
 # tandemDups (DONE - 2021-05-12 - Hiram)
     mkdir /hive/data/genomes/canFam6/bed/tandemDups
     cd /hive/data/genomes/canFam6/bed/tandemDups
     time (~/kent/src/hg/utils/automation/doTandemDup.pl \
   -twoBit=/hive/data/genomes/canFam6/canFam6.unmasked.2bit canFam6) \
         > do.log 2>&1 &
     # real    172m17.400s
 
     cat fb.canFam6.tandemDups.txt
     # 38991000 bases of 2312802198 (1.686%) in intersection
 
     bigBedInfo canFam6.tandemDups.bb | sed -e 's/^/#  /;'
 #  version: 4
 #  fieldCount: 13
 #  hasHeaderExtension: yes
 #  isCompressed: yes
 #  isSwapped: 0
 #  extraIndexCount: 0
 #  itemCount: 657,594
 #  primaryDataSize: 17,541,691
 #  primaryIndexSize: 53,796
 #  zoomLevels: 8
 #  chromCount: 84
 #  basesCovered: 1,396,340,438
 #  meanDepth (of bases covered): 4.667856
 #  minDepth: 1.000000
 #  maxDepth: 251.000000
 #  std of depth: 8.938384
 
 #########################################################################
 # ucscToINSDC and ucscToRefSeq table/track (DONE - 2021-05-13 - Hiram)
     # construct idKeys for the genbank sequence
     mkdir /hive/data/genomes/canFam6/refseq/idKeys
     cd /hive/data/genomes/canFam6/refseq/idKeys
     faToTwoBit ../GCF_*a_genomic.fna.gz canFam6.refseq.2bit
 
     time (doIdKeys.pl -buildDir=`pwd` \
         -twoBit=`pwd`/canFam6.refseq.2bit refseqCanFam6)  > do.log 2>&1 &
     # real    0m33.413s
 
     cat refseqCanFam6.keySignature.txt
     #  efdede185d06fdca97de518811962150
 
     mkdir -p /hive/data/genomes/canFam6/genbank/idKeys
     cd /hive/data/genomes/canFam6/genbank/idKeys
     ln -s /hive/data/outside/ncbi/genomes/GCA/000/002/285/GCA_000002285.4_Dog10K_Boxer_Tasha/GCA_000002285.4_Dog10K_Boxer_Tasha_genomic.fna.gz .
     faToTwoBit GCA*.fna.gz canFam6.genbank.2bit
     time (doIdKeys.pl -buildDir=`pwd` \
         -twoBit=`pwd`/canFam6.genbank.2bit genbankCanFam6)  > do.log 2>&1 &
     # real    0m32.596s
 
     cat genbankCanFam6.keySignature.txt
     #  ec6e932a9b4aa21e9603895931320f13
 
     mkdir /hive/data/genomes/canFam6/bed/chromAlias
     cd /hive/data/genomes/canFam6/bed/chromAlias
 
     join -t$'\t' ../idKeys/canFam6.idKeys.txt \
         ../../genbank/idKeys/genbankCanFam6.idKeys.txt | cut -f2- \
           | sort -k1,1 | join -t$'\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$'\t' ../idKeys/canFam6.idKeys.txt \
         ../../refseq/idKeys/refseqCanFam6.idKeys.txt | cut -f2- \
           | sort -k1,1 | join -t$'\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
 
     # lookup the genbank accession for chrM NC_002008.4 -> U96639.2
     # add it to the INSDC names:
     printf "chrM\t0\t16727\tU96639.2\n" >> ucscToINSDC.bed
 
     # should be same line counts throughout:
     wc -l * ../../chrom.sizes
     #	147 ucscToINSDC.bed
     #	147 ucscToRefSeq.bed
     #	147 ../../chrom.sizes
 
     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 canFam6 ucscToINSDC stdin ucscToINSDC.bed
     export chrSize=`cut -f1 ucscToRefSeq.bed | awk '{print length($0)}' | sort -n | tail -1`
     echo $chrSize
     sed -e "s/21/$chrSize/" $HOME/kent/src/hg/lib/ucscToINSDC.sql \
        | sed -e 's/INSDC/RefSeq/g;' \
          | hgLoadSqlTab canFam6 ucscToRefSeq stdin ucscToRefSeq.bed
 
     # should be quiet for all OK
     checkTableCoords canFam6 ucscToINSDC
     checkTableCoords canFam6 ucscToRefSeq
 
     # should cover %100 entirely:
     featureBits -countGaps canFam6 ucscToINSDC
     #  2312802198 bases of 2312802198 (100.000%) in intersection
     featureBits -countGaps canFam6 ucscToRefSeq
     #  2312802198 bases of 2312802198 (100.000%) in intersection
 
 #########################################################################
 # add chromAlias table (DONE - 2021-05-13 - Hiram)
 
     mkdir /hive/data/genomes/canFam6/bed/chromAlias
     cd /hive/data/genomes/canFam6/bed/chromAlias
 
     grep -v "^#" ../../refseq/G*_assembly_report.txt \
         | awk '{printf "%s\t%s\n", $5,$1}' | sort > ncbi.genbank.txt
     grep -v "^#" ../../refseq/G*_assembly_report.txt \
         | awk '{printf "%s\t%s\n", $7,$1}' | sort > ncbi.refseq.txt
 
     hgsql -N -e 'select chrom,name from ucscToINSDC;' canFam6 \
         | sort -k1,1 > ucsc.genbank.tab
     hgsql -N -e 'select chrom,name from ucscToRefSeq;' canFam6 \
         | sort -k1,1 > ucsc.refseq.tab
 
     # the awk removes lines where the UCSC name is identical to the NCBI name
     join -t$'\t' -1 2 <(sort -k2,2 ucsc.refseq.tab) ncbi.refseq.txt \
       | cut -f2-3 | awk '$1 != $2' | sort > ucsc.assembly.tab
 
     wc -l * ../../chrom.sizes
     #   147 ncbi.genbank.txt
     #   147 ncbi.refseq.txt
     #   147 ucsc.assembly.tab
     #   147 ucsc.genbank.tab
     #   147 ucsc.refseq.tab
     #   147 ../../chrom.sizes
 
     # assembly counts are smaller since equivalence has been eliminated
 
     ~/kent/src/hg/utils/automation/chromAlias.pl ucsc.*.tab \
         > canFam6.chromAlias.tab
 
 for t in refseq genbank assembly
 do
   c0=`cat ucsc.$t.tab | wc -l`
   c1=`grep $t canFam6.chromAlias.tab | wc -l`
   ok="OK"
   if [ "$c0" -ne "$c1" ]; then
      ok="ERROR"
   fi
   printf "# checking $t: $c0 =? $c1 $ok\n"
 done
 # checking refseq: 147 =? 147 OK
 # checking genbank: 147 =? 147 OK
 # checking assembly: 147 =? 147 OK
 
     # verify chrM is here properly:
     grep chrM canFam6.chromAlias.tab 
 # MT      chrM    assembly
 # NC_002008.4     chrM    refseq
 # U96639.2        chrM    genbank
 
     hgLoadSqlTab canFam6 chromAlias ~/kent/src/hg/lib/chromAlias.sql \
         canFam6.chromAlias.tab
 
 #########################################################################
 # fixup search rule for assembly track/gold table (DONE - 2021-05-13 - Hiram)
     cd ~/kent/src/hg/makeDb/trackDb/dog/canFam6
     # preview prefixes and suffixes:
     hgsql -N -e "select frag from gold;" canFam6 \
       | sed -e 's/[0-9_.]\+//;' | sort | uniq -c 
    1174 AAEX
       1 NC
 
     # implies a rule: '[AN][AC][EX0-9_]+(\.[0-9_]+)?'
 
     # verify this rule will find them all and eliminate them all:
     hgsql -N -e "select frag from gold;" canFam6 | wc -l
     # 1175
 
     hgsql -N -e "select frag from gold;" canFam6 \
        | egrep -e '[AN][AC][EX0-9_]+(\.[0-9_]+)?' | wc -l
     # 1175
 
     hgsql -N -e "select frag from gold;" canFam6 \
        | egrep -v -e '[AN][AC][EX0-9_]+(\.[0-9_]+)?' | wc -l
     # 0
 
     # hence, add to trackDb/rhesus/canFam6/trackDb.ra
 searchTable gold
 shortCircuit 1
 termRegex [AN][AC][EX0-9_]+(\.[0-9_]+)?
 query select chrom,chromStart,chromEnd,frag from %s where frag like '%s%%'
 searchPriority 8
 
     # verify searches work in the position box
 
     git commit -m 'adding search rule for gold/assembly track refs #27546' \
        trackDb.ra
 
 ##########################################################################
 # running repeat masker (DONE - 2021-05-12 - Hiram)
     mkdir /hive/data/genomes/canFam6/bed/repeatMasker
     cd /hive/data/genomes/canFam6/bed/repeatMasker
     time  (doRepeatMasker.pl -buildDir=`pwd` \
         -bigClusterHub=ku -dbHost=hgwdev -workhorse=hgwdev \
         -smallClusterHub=ku canFam6) > do.log 2>&1
     # real    294m16.121s
 
     cat faSize.rmsk.txt
 # 2312802198 bases (58852 N's 2312743346 real 1340725791 upper
 #	972017555 lower) in 147 sequences in 1 files
 # Total size: mean 15733348.3 sd 28607349.9 min 551 (chrUn_NW_023329752v1)
 #	max 122014068 (chr1) median 7637
 # %42.03 masked total, %42.03 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;           
 
     sed -e 's/^/# /;' versionInfo.txt 
 # The repeat files provided for this assembly were generated using RepeatMasker.
 #   Smit, AFA, Hubley, R & Green, P.,
 #   RepeatMasker Open-4.0.
 #   1996-2010 <http://www.repeatmasker.org>.
 # 
 # VERSION:
 # RepeatMasker version development-$Id: RepeatMasker,v 1.332 2017/04/17 19:01:11 rhubley Exp $
 # Search Engine: Crossmatch [ 1.090518 ]
 # Master RepeatMasker Database: /hive/data/staging/data/RepeatMasker181121/Libraries/RepeatMaskerLib.embl ( Complete Database: dc20181026-rb20181026 )
 # 
 # 
 # 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;                                   *
 # # RepeatMasker engine: -engine crossmatch -s
 # # RepeatMasker library options: -species 'Canis lupus familiaris'
 # 
 # PARAMETERS:
 # /hive/data/staging/data/RepeatMasker/RepeatMasker -engine crossmatch -s -align -species 'Canis lupus familiaris'
 
     time featureBits -countGaps canFam6 rmsk
     # 972021595 bases of 2312802198 (42.028%) in intersection
     # real    0m34.798s
 
     # 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;' canFam6 \
         | bedSingleCover.pl stdin | ave -col=4 stdin | grep "^total"
     # total 972021595.000000
     # real    0m21.176s
 
 ##########################################################################
 # running simple repeat (DONE - 2021-05-12 - Hiram)
 
     mkdir /hive/data/genomes/canFam6/bed/simpleRepeat
     cd /hive/data/genomes/canFam6/bed/simpleRepeat
     time (doSimpleRepeat.pl -buildDir=`pwd` -bigClusterHub=ku \
         -dbHost=hgwdev -workhorse=hgwdev -smallClusterHub=ku \
         -trf409=6 canFam6) > do.log 2>&1
     # real    73m21.349s
 
     cat fb.simpleRepeat
     # 47306497 bases of 2312743346 (2.045%) in intersection
 
     cd /hive/data/genomes/canFam6
     # if using the Window Masker result:
     cd /hive/data/genomes/canFam6
 #    twoBitMask bed/windowMasker/canFam6.cleanWMSdust.2bit \
 #       -add bed/simpleRepeat/trfMask.bed  canFam6.2bit
     #   you can safely ignore the warning about fields >= 13
 
     # add to rmsk after it is done:
     twoBitMask canFam6.rmsk.2bit \
         -add bed/simpleRepeat/trfMask.bed canFam6.2bit
     #   you can safely ignore the warning about fields >= 13
     twoBitToFa canFam6.2bit stdout | faSize stdin > faSize.canFam6.2bit.txt
     cat faSize.canFam6.2bit.txt
 # 2312802198 bases (58852 N's 2312743346 real 1338850957 upper
 #	973892389 lower) in 147 sequences in 1 files
 # Total size: mean 15733348.3 sd 28607349.9 min 551 (chrUn_NW_023329752v1)
 #	max 122014068 (chr1) median 7637
 # %42.11 masked total, %42.11 masked real
 
     rm /gbdb/canFam6/canFam6.2bit
     ln -s `pwd`/canFam6.2bit /gbdb/canFam6/canFam6.2bit
 
 #########################################################################
 # CREATE MICROSAT TRACK (DONE - 2021-05-12 - Hiram)
     ssh hgwdev
     mkdir /cluster/data/canFam6/bed/microsat
     cd /cluster/data/canFam6/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 canFam6 microsat microsat.bed
     # Read 56108 elements of size 4 from microsat.bed
 
 ##########################################################################
 ## WINDOWMASKER (DONE - 2021-05-12 - Hiram)
 
     mkdir /hive/data/genomes/canFam6/bed/windowMasker
     cd /hive/data/genomes/canFam6/bed/windowMasker
     time (doWindowMasker.pl -buildDir=`pwd` -workhorse=hgwdev \
         -dbHost=hgwdev canFam6) > do.log 2>&1
     # real    89m33.579s
 
     # Masking statistics
     cat faSize.canFam6.cleanWMSdust.txt
 # 2312802198 bases (58852 N's 2312743346 real 1546969439 upper
 #	765773907 lower) in 147 sequences in 1 files
 # Total size: mean 15733348.3 sd 28607349.9 min 551 (chrUn_NW_023329752v1)
 #	max 122014068 (chr1) median 7637
 # %33.11 masked total, %33.11 masked real
 
     featureBits -countGaps canFam6 rmsk windowmaskerSdust \
        2> fb.canFam6.rmsk.windowmaskerSdust.txt
     cat fb.canFam6.rmsk.windowmaskerSdust.txt
     # 517620731 bases of 2312802198 (22.381%) in intersection
 
     time (doWindowMasker.pl -buildDir=`pwd` -workhorse=hgwdev \
         -continue=cleanup -dbHost=hgwdev canFam6) > cleanup.log 2>&1
 
 ##########################################################################
 # cpgIslands - (DONE - 2021-05-13 - Hiram)
     mkdir /hive/data/genomes/canFam6/bed/cpgIslands
     cd /hive/data/genomes/canFam6/bed/cpgIslands
     time (doCpgIslands.pl -dbHost=hgwdev -bigClusterHub=ku \
       -workhorse=hgwdev -smallClusterHub=ku canFam6) > do.log 2>&1
     # real    2m52.170s
 
     cat fb.canFam6.cpgIslandExt.txt
     # 44591675 bases of 2312743346 (1.928%) in intersection
 
 ##############################################################################
 # genscan - (DONE - 2021-05-13 - Hiram)
     mkdir /hive/data/genomes/canFam6/bed/genscan
     cd /hive/data/genomes/canFam6/bed/genscan
     time (doGenscan.pl -buildDir=`pwd` -workhorse=hgwdev -dbHost=hgwdev \
       -bigClusterHub=ku canFam6) > do.log 2>&1
     # real    48m34.968s
 
     sed -e 's/^/    # /;' fb.canFam6.genscan.txt
     # 54159469 bases of 2312743346 (2.342%) in intersection
     sed -e 's/^/    # /;' fb.canFam6.genscanSubopt.txt
     # 46763127 bases of 2312743346 (2.022%) in intersection
 
 #########################################################################
 # Create kluster run files (DONE - 2021-05-13 - Hiram)
 
     # numerator is canFam6 gapless bases "real" as reported by:
     featureBits -noRandom -noHap canFam6 gap
     # 58852 bases of 2310615395 (0.003%) 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 \( 2310615395 / 2861349177 \) \* 1024
     #  ( 2310615395 / 2861349177 ) * 1024 = 826.907175
 
     # ==> use -repMatch=800 according to size scaled down from 1024 for human.
     #   and rounded down to nearest 50
     cd /hive/data/genomes/canFam6
     time blat canFam6.2bit \
          /dev/null /dev/null -tileSize=11 -makeOoc=jkStuff/canFam6.11.ooc \
         -repMatch=800
     # Wrote 28074 overused 11-mers to jkStuff/canFam6.11.ooc
     # real    0m24.061s
 
     # canFam5 at repMatch=800:
     #   Wrote 28510 overused 11-mers to jkStuff/canFam5.11.ooc
 
     # canFam4 at repMatch=800:
     #	Wrote 34718 overused 11-mers to jkStuff/canFam4.11.ooc
 
     # canFam3 at repMatch=900:
     #   Wrote 24788 overused 11-mers to jkStuff/canFam3.11.ooc
     #	real    1m11.629s
 
     #   there are no non-bridged gaps
     hgsql -N \
         -e 'select * from gap where bridge="no" order by size;' canFam6
     hgsql -N -e 'select size from gap where bridge="no" order by size;' \
 	canFam6  | sort | uniq -c | sort -k2,2n | sed -e 's/^/# /;'
 
     # survey gap sizes:
     hgsql -N -e 'select size from gap where bridge="yes" order by size;' \
        canFam6  | ave stdin | sed -e 's/^/# /;'
 # Q1 25.000000
 # median 25.000000
 # Q3 100.000000
 # average 57.249027
 # min 1.000000
 # max 100.000000
 # count 1028
 # total 58852.000000
 # standard deviation 37.486982
 
     # and survey these gaps:
      hgsql -N -e \
        'select size from gap where bridge="yes" order by size;' canFam6 \
           | sort | uniq -c | sed -e 's/^/# /;'
 #      13 1
 #       4 10
 #     444 100
 #       1 19
 #     556 25
 #       1 31
 #       1 34
 #       1 38
 #       1 40
 #       1 50
 #       1 54
 #       1 56
 #       1 57
 #       2 60
 
     # using ordinary gaps to make a lift file
     # with minimum gap size at 100
     gapToLift -allowBridged -verbose=2 -minGap=100 canFam6 \
 	jkStuff/canFam6.gaps.lft -bedFile=jkStuff/canFam6.gaps.bed
 
     wc -l jkStuff/*gaps*
     # 591 jkStuff/canFam6.gaps.bed
     # 591 jkStuff/canFam6.gaps.lft
 
     # to see the gaps used:
     bedInvert.pl chrom.sizes jkStuff/canFam6.gaps.bed | less
     # and their sizes:
     bedInvert.pl chrom.sizes jkStuff/canFam6.gaps.bed \
 	| cut -f4 | sort -n | uniq -c | less
     #     444 100
 
 ########################################################################
 # lastz/chain/net swap human/hg38 (TBD - 2020-07-29 - Hiram)
 
     # original alignment
     cd /hive/data/genomes/hg38/bed/lastzCanFam6.2020-07-29
 
     cat fb.hg38.chainCanFam6Link.txt
     # 1545648756 bases of 3110768607 (49.687%) in intersection
     cat fb.hg38.chainSynCanFam6Link.txt
     # 1484758745 bases of 3110768607 (47.730%) in intersection
     cat fb.hg38.chainRBest.CanFam6.txt
     # 1422619513 bases of 3110768607 (45.732%) in intersection
 
     # and for the swap:
     mkdir /hive/data/genomes/canFam6/bed/blastz.hg38.swap
     cd /hive/data/genomes/canFam6/bed/blastz.hg38.swap
 
     time (doBlastzChainNet.pl -verbose=2 \
       /hive/data/genomes/hg38/bed/lastzCanFam6.2020-07-29/DEF \
         -swap -chainMinScore=3000 -chainLinearGap=medium \
           -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
             -syntenicNet) > swap.log 2>&1
     #  real    78m37.078s
 
     cat fb.canFam6.chainHg38Link.txt
     # 1460025525 bases of 2337131234 (62.471%) in intersection
     cat fb.canFam6.chainSynHg38Link.txt
     # 1423305734 bases of 2337131234 (60.900%) in intersection
 
     time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \
 	canFam6 hg38) > rbest.log 2>&1 &
     # real    255m9.076s
 
     cat fb.canFam6.chainRBest.Hg38.txt
     # 1422612399 bases of 2337131234 (60.870%) in intersection
 
 ############################################################################
 # lastz/chain/net swap mouse/mm10 (TBD - 2020-07-29 - Hiram)
 
     # original alignment
     cd /hive/data/genomes/mm10/bed/lastzCanFam6.2020-07-29
 
     cat fb.mm10.chainCanFam6Link.txt
     #	776486006 bases of 2652783500 (29.271%) in intersection
     cat fb.mm10.chainSynCanFam6Link.txt
     #   735561772 bases of 2652783500 (27.728%) in intersection
     cat fb.mm10.chainRBest.CanFam6.txt
     # 740117947 bases of 2652783500 (27.900%) in intersection
 
     mkdir /hive/data/genomes/canFam6/bed/blastz.mm10.swap
     cd /hive/data/genomes/canFam6/bed/blastz.mm10.swap
 
     time (doBlastzChainNet.pl -verbose=2 \
 	/hive/data/genomes/mm10/bed/lastzCanFam6.2020-07-29/DEF \
 	-swap -syntenicNet \
 	-workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
 	-chainMinScore=3000 -chainLinearGap=medium) > swap.log 2>&1 &
     #	real    44m9.935s
 
     cat fb.canFam6.chainMm10Link.txt
     #	759821061 bases of 2337131234 (32.511%) in intersection
     cat fb.canFam6.chainSynMm10Link.txt
     #   731350605 bases of 2337131234 (31.293%) in intersection
 
     time (doRecipBest.pl -load -workhorse=hgwdev canFam6 mm10 \
       -buildDir=`pwd` -workhorse=hgwdev) > rbest.log 2>&1 &
     # real    162m30.634s
 
     cat fb.canFam6.chainRBest.Mm10.txt
     # 739177732 bases of 2337131234 (31.628%) in intersection
 
 ############################################################################
 # lastz/chain/net swap mouse/mm39 (TBD - 2020-08-17 - Hiram)
 
     # original alignment
     cd /hive/data/genomes/mm39/bed/lastzCanFam6.2020-08-17
     cat fb.mm39.chainCanFam6Link.txt
     #	778327929 bases of 2654624157 (29.320%) in intersection
     cat fb.mm39.chainSynCanFam6Link.txt
     #   735515331 bases of 2654624157 (27.707%) in intersection
     cat fb.mm39.chainRBest.CanFam6.txt
     # 740738480 bases of 2654624157 (27.904%) in intersection
 
     mkdir /hive/data/genomes/canFam6/bed/blastz.mm39.swap
     cd /hive/data/genomes/canFam6/bed/blastz.mm39.swap
     time (doBlastzChainNet.pl -verbose=2 \
 	/hive/data/genomes/mm39/bed/lastzCanFam6.2020-08-17/DEF \
 	-swap -syntenicNet \
 	-workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
 	-chainMinScore=3000 -chainLinearGap=medium) > swap.log 2>&1 &
     #	real    44m12.732s
 
     cat fb.canFam6.chainMm39Link.txt
     #	762233776 bases of 2337131234 (32.614%) in intersection
     cat fb.canFam6.chainSynMm39Link.txt
     #   731337903 bases of 2337131234 (31.292%) in intersection
 
     time (doRecipBest.pl -load -workhorse=hgwdev canFam6 mm39 \
       -buildDir=`pwd` -workhorse=hgwdev) > rbest.log 2>&1 &
     # real    174m14.398s
 
     cat fb.canFam6.chainRBest.Mm39.txt
     # 739648625 bases of 2337131234 (31.648%) in intersection
 
 ##############################################################################
 # GENBANK AUTO UPDATE (DONE - 2021-05-13 - Hiram)
     ssh hgwdev
     cd $HOME/kent/src/hg/makeDb/genbank
     git pull
     # /cluster/data/genbank/data/organism.lst shows:
     # organism       mrnaCnt estCnt  refSeqCnt
     # Canis latrans   2       0       0
     # Canis lupus     36      0       0
     # Canis lupus familiaris  3371    382652  1723
     # Canis lupus laniger     2       0       0
     # Canis lupus lupus       2       0       0
     # Canis mesomelas 1       0       0
     # Canis sp.       45      0       0
 
     # the latrans is the Coyota, the mesomelas
     # is the Black-backed jackal from Africa and the langier is the Tibetan wolf
     # lupus lupus is the Eurasian wolf
 
     # edit etc/genbank.conf to add canFam6 just after canFam5
 
 # canFam6 (GCF_000002285.5 Dog10K Boxer Tasha)
 canFam6.serverGenome = /hive/data/genomes/canFam6/canFam6.2bit
 canFam6.ooc = /hive/data/genomes/canFam6/jkStuff/canFam6.11.ooc
 canFam6.lift = /hive/data/genomes/canFam6/jkStuff/canFam6.gaps.lft
 canFam6.align.unplacedChroms = chrUn_*
 canFam6.refseq.mrna.native.pslCDnaFilter  = ${finished.refseq.mrna.native.pslCDnaFilter}
 canFam6.refseq.mrna.xeno.pslCDnaFilter    = ${finished.refseq.mrna.xeno.pslCDnaFilter}
 canFam6.genbank.mrna.native.pslCDnaFilter = ${finished.genbank.mrna.native.pslCDnaFilter}
 canFam6.genbank.mrna.xeno.pslCDnaFilter   = ${finished.genbank.mrna.xeno.pslCDnaFilter}
 canFam6.genbank.est.native.pslCDnaFilter  = ${finished.genbank.est.native.pslCDnaFilter}
 canFam6.refseq.mrna.native.load = yes
 canFam6.refseq.mrna.xeno.load = yes
 # DO NOT NEED genbank.mrna.xeno except for human, mouse
 canFam6.genbank.mrna.xeno.load = yes
 canFam6.downloadDir = canFam6
 canFam6.upstreamGeneTbl = refGene
 canFam6.perChromTables = no
 
     # verify the files specified exist before checking in the file:
   grep ^canFam6 etc/genbank.conf | grep hive | awk '{print $NF}' | xargs ls -og
 # -rw-rw-r-- 1 607528981 May 12 22:06 /hive/data/genomes/canFam6/canFam6.2bit
 # -rw-rw-r-- 1    112304 May 13 10:40 /hive/data/genomes/canFam6/jkStuff/canFam6.11.ooc
 # -rw-rw-r-- 1     24204 May 13 10:48 /hive/data/genomes/canFam6/jkStuff/canFam6.gaps.lft
 
     git commit -m "Added canFam6 dog; refs #27546" 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 canFam6 to:
     #   etc/hgwdev.dbs etc/align.dbs
     git commit -m "Added canFam6 - dog refs #27546" etc/hgwdev.dbs etc/align.dbs
     git push
     make etc-update
 
     # Notify Chris Lee this is ready to go.  Magic will happen.
 
 #############################################################################
 # augustus gene track (DONE - 2021-05-13 - Hiram)
 
     mkdir /hive/data/genomes/canFam6/bed/augustus
     cd /hive/data/genomes/canFam6/bed/augustus
     time (doAugustus.pl -buildDir=`pwd` -bigClusterHub=ku \
         -species=human -dbHost=hgwdev \
            -workhorse=hgwdev canFam6) > do.log 2>&1
     # real    114m7.669s
 
     sed -e 's/^/    # /;' fb.canFam6.augustusGene.txt
     # 47489256 bases of 2312743346 (2.053%) in intersection
 
 #########################################################################
 # ncbiRefSeq (DONE - 2021-05-13 - Hiram)
 
     mkdir /hive/data/genomes/canFam6/bed/ncbiRefSeq
     cd /hive/data/genomes/canFam6/bed/ncbiRefSeq
     # running step wise just to be careful
     time (~/kent/src/hg/utils/automation/doNcbiRefSeq.pl -buildDir=`pwd` \
       -bigClusterHub=ku -dbHost=hgwdev \
       -stop=download -fileServer=hgwdev -smallClusterHub=ku -workhorse=hgwdev \
       GCF_000002285.5_Dog10K_Boxer_Tasha canFam6) > download.log 2>&1
     # real    2m5.429s
 
     time (~/kent/src/hg/utils/automation/doNcbiRefSeq.pl -buildDir=`pwd` \
       -continue=process -bigClusterHub=ku -dbHost=hgwdev \
       -stop=process -fileServer=hgwdev -smallClusterHub=ku -workhorse=hgwdev \
       GCF_000002285.5_Dog10K_Boxer_Tasha canFam6) > process.log 2>&1
     # real    3m31.265s
 
     time (~/kent/src/hg/utils/automation/doNcbiRefSeq.pl -buildDir=`pwd` \
       -continue=load -bigClusterHub=ku -dbHost=hgwdev \
       -fileServer=hgwdev -smallClusterHub=ku -workhorse=hgwdev \
       GCF_000002285.5_Dog10K_Boxer_Tasha canFam6) > load.log 2>&1
     # real    0m47.905s
 
     cat fb.ncbiRefSeq.canFam6.txt
     #  88916188 bases of 2312743346 (3.845%) in intersection
 
     # add: include ../../refSeqComposite.ra alpha
     # to the dog/canFam6/trackDb.ra to turn on the track in the browser
 
     featureBits -enrichment canFam6 refGene ncbiRefSeq 
 # refGene 0.138%, ncbiRefSeq 3.845%, both 0.136%, cover 99.15%, enrich 25.79x
     featureBits -enrichment canFam6 ncbiRefSeq refGene
 # ncbiRefSeq 3.845%, refGene 0.138%, both 0.136%, cover 3.55%, enrich 25.79x
     featureBits -enrichment canFam6 ncbiRefSeqCurated refGene
 # ncbiRefSeqCurated 0.152%, refGene 0.138%, both 0.133%, cover 87.51%, enrich 636.15x
     featureBits -enrichment canFam6 refGene ncbiRefSeqCurated
  # refGene 0.138%, ncbiRefSeqCurated 0.152%, both 0.133%, cover 96.65%, enrich 636.15x
 
 #########################################################################
 # LIFTOVER TO canFam5 (DONE - 2021-05-13 - Hiram)
     ssh hgwdev
     mkdir /hive/data/genomes/canFam6/bed/blat.canFam5.2021-05-13
     cd /hive/data/genomes/canFam6/bed/blat.canFam5.2021-05-13
     doSameSpeciesLiftOver.pl -verbose=2 \
         -debug -bigClusterHub=ku -dbHost=hgwdev -workhorse=hgwdev \
         -ooc=/hive/data/genomes/canFam6/jkStuff/canFam6.11.ooc \
          canFam6 canFam5
     time (doSameSpeciesLiftOver.pl -verbose=2 \
         -bigClusterHub=ku -dbHost=hgwdev -workhorse=hgwdev \
         -ooc=/hive/data/genomes/canFam6/jkStuff/canFam6.11.ooc \
          canFam6 canFam5) > doLiftOverToCanFam5.log 2>&1
     # real    179m37.613s
 
     # see if the liftOver menus function in the browser from canFam6 to canFam5
 
 #########################################################################
 # LIFTOVER TO canFam4 (DONE - 2021-05-13 - Hiram)
     ssh hgwdev
     mkdir /hive/data/genomes/canFam6/bed/blat.canFam4.2021-05-13
     cd /hive/data/genomes/canFam6/bed/blat.canFam4.2021-05-13
     doSameSpeciesLiftOver.pl -verbose=2 \
         -debug -bigClusterHub=ku -dbHost=hgwdev -workhorse=hgwdev \
         -ooc=/hive/data/genomes/canFam6/jkStuff/canFam6.11.ooc \
          canFam6 canFam4
     time (doSameSpeciesLiftOver.pl -verbose=2 \
         -bigClusterHub=ku -dbHost=hgwdev -workhorse=hgwdev \
         -ooc=/hive/data/genomes/canFam6/jkStuff/canFam6.11.ooc \
          canFam6 canFam4) > doLiftOverToCanFam4.log 2>&1
     # real    960m7.335s
 
     # see if the liftOver menus function in the browser from canFam6 to canFam4
 
 #########################################################################
 # LIFTOVER TO canFam3 (DONE - 2021-05-13 - Hiram)
     ssh hgwdev
     mkdir /hive/data/genomes/canFam6/bed/blat.canFam3.2021-05-13
     cd /hive/data/genomes/canFam6/bed/blat.canFam3.2021-05-13
     doSameSpeciesLiftOver.pl -verbose=2 \
         -debug -bigClusterHub=ku -dbHost=hgwdev -workhorse=hgwdev \
         -ooc=/hive/data/genomes/canFam6/jkStuff/canFam6.11.ooc \
          canFam6 canFam3
     time (doSameSpeciesLiftOver.pl -verbose=2 \
         -bigClusterHub=ku -dbHost=hgwdev -workhorse=hgwdev \
         -ooc=/hive/data/genomes/canFam6/jkStuff/canFam6.11.ooc \
          canFam6 canFam3) > doLiftOverToCanFam3.log 2>&1
     # real    2695m19.425s
 
     # see if the liftOver menus function in the browser from canFam6 to canFam3
 
 #########################################################################
 #  BLATSERVERS ENTRY (DONE - 2021-05-13 - Hiram)
     mkdir /hive/data/genomes/canFam6/dynamicBlat
     cd /hive/data/genomes/canFam6/dynamicBlat
 
     time gfServer -trans index canFam6.trans.gfidx ../canFam6.2bit &
     # real    5m27.906s
     time gfServer -stepSize=5 index canFam6.untrans.gfidx ../canFam6.2bit
     # real    3m3.944s
 
     rsync -a -P ../canFam6.2bit qateam@dynablat-01:/scratch/hubs/canFam6/
     rsync -a -P canFam6.untrans.gfidx qateam@dynablat-01:/scratch/hubs/canFam6/
     rsync -a -P canFam6.trans.gfidx qateam@dynablat-01:/scratch/hubs/canFam6/
 
  hgsql -e 'INSERT INTO blatServers (db, host, port, isTrans, canPcr, dynamic) \
 	VALUES ("canFam6", "dynablat-01", "4040", "1", "0", "1"); \
 	INSERT INTO blatServers (db, host, port, isTrans, canPcr, dynamic) \
 	VALUES ("canFam6", "dynablat-01", "4040", "0", "1", "1");' \
 	    hgcentraltest
     #	test it with some sequence, for example ACE2:
 
 >hg38_ACE2
 MSSSSWLLLSLVAVTAAQSTIEEQAKTFLDKFNHEAEDLFYQSSLASWNYNTNITEENVQ
 NMNNAGDKWSAFLKEQSTLAQMYPLQEIQNLTVKLQLQALQQNGSSVLSEDKSKRLNTIL
 NTMSTIYSTGKVCNPDNPQECLLLEPGLNEIMANSLDYNERLWAWESWRSEVGKQLRPLY
 EEYVVLKNEMARANHYEDYGDYWRGDYEVNGVDGYDYSRGQLIEDVEHTFEEIKPLYEHL
 HAYVRAKLMNAYPSYISPIGCLPAHLLGDMWGRFWTNLYSLTVPFGQKPNIDVTDAMVDQ
 AWDAQRIFKEAEKFFVSVGLPNMTQGFWENSMLTDPGNVQKAVCHPTAWDLGKGDFRILM
 CTKVTMDDFLTAHHEMGHIQYDMAYAAQPFLLRNGANEGFHEAVGEIMSLSAATPKHLKS
 IGLLSPDFQEDNETEINFLLKQALTIVGTLPFTYMLEKWRWMVFKGEIPKDQWMKKWWEM
 KREIVGVVEPVPHDETYCDPASLFHVSNDYSFIRYYTRTLYQFQFQEALCQAAKHEGPLH
 KCDISNSTEAGQKLFNMLRLGKSEPWTLALENVVGAKNMNVRPLLNYFEPLFTWLKDQNK
 NSFVGWSTDWSPYADQSIKVRISLKSALGDKAYEWNDNEMYLFRSSVAYAMRQYFLKVKN
 QMILFGEEDVRVANLKPRISFNFFVTAPKNVSDIIPRTEVEKAIRMSRSRINDAFRLNDN
 SLEFLGIQPTLGPPNQPPVSIWLIVFGVVMGVIVVGIVILIFTGIRDRKKKNKARSGENP
 YASIDISKGENNPGFQNTDDVQTSF
 
 ############################################################################
 ## reset default position to gene: ACE2 as found by blat of human protein
 ##  (DONE - 2021-05-13 - Hiram)
 
     ssh hgwdev
     hgsql -e 'update dbDb set defaultPos="chrX:11706333-11735291"
 	where name="canFam6";' hgcentraltest
 
 ##############################################################################
 # crispr whole genome (DONE - 2021-05-13 - Hiram)
     mkdir /hive/data/genomes/canFam6/bed/crisprAll
     cd /hive/data/genomes/canFam6/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 \
     canFam6 -tableName=crisprAll \
     -fileServer=hgwdev \
     -buildDir=`pwd` -smallClusterHub=hgwdev -bigClusterHub=ku \
       -workhorse=hgwdev) > indexFa.log 2>&1
     # real    58m27.340s
     # that command failed, finished the final command manually, it needed
     # the gene table on the python command
 
     time (~/kent/src/hg/utils/automation/doCrispr.pl -verbose=2 \
     -continue=ranges canFam6 -tableName=crisprAll \
     -fileServer=hgwdev \
     -buildDir=`pwd` -smallClusterHub=hgwdev -bigClusterHub=ku \
       -workhorse=hgwdev) > ranges.log 2>&1
     # real    8554m11.613s
 
     cat guides/run.time | sed -e 's/^/# /;'
 # Completed: 100 of 100 jobs
 # CPU time in finished jobs:      10613s     176.88m     2.95h    0.12d  0.000 y
 # IO & Wait Time:                   318s       5.30m     0.09h    0.00d  0.000 y
 # Average job time:                 109s       1.82m     0.03h    0.00d
 # Longest finished job:             269s       4.48m     0.07h    0.00d
 # Submission to last job:           272s       4.53m     0.08h    0.00d
 
     cat specScores/run.time | sed -e 's/^/# /;'
 # Completed: 3079460 of 3079460 jobs
 # CPU time in finished jobs:  246730604s 4112176.74m 68536.28h 2855.68d  7.824 y
 # IO & Wait Time:               5517084s   91951.39m  1532.52h   63.86d  0.175 y
 # Average job time:                  82s       1.37m     0.02h    0.00d
 # Longest finished job:             160s       2.67m     0.04h    0.00d
 # Submission to last job:        276754s    4612.57m    76.88h    3.20d
 
     grep "Number of" ranges.log | grep Scores | grep "^#"
 # Number of specScores: 231915228
 # Number of effScores: 253445228
 
     cat effScores/run.time | sed -e 's/^/# /;'
 # Completed: 25340 of 25340 jobs
 # CPU time in finished jobs:   13149467s  219157.78m  3652.63h  152.19d  0.417 y
 # IO & Wait Time:                145678s    2427.97m    40.47h    1.69d  0.005 y
 # Average job time:                 525s       8.74m     0.15h    0.01d
 # Longest finished job:           97897s    1631.62m    27.19h    1.13d
 # Submission to last job:        110740s    1845.67m    30.76h    1.28d
 
     cat offTargets/run.time | sed -e 's/^/# /;'
 # Completed: 153974 of 153974 jobs
 # CPU time in finished jobs:    1850764s   30846.07m   514.10h   21.42d  0.059 y
 # IO & Wait Time:               1927940s   32132.33m   535.54h   22.31d  0.061 y
 # Average job time:                  25s       0.41m     0.01h    0.00d
 # Longest finished job:              64s       1.07m     0.02h    0.00d
 # Submission to last job:          3954s      65.90m     1.10h    0.05d
 
 #########################################################################
 # all.joiner update, downloads and in pushQ - (WORKING - 2019-11-20 - Hiram)
     cd $HOME/kent/src/hg/makeDb/schema
     # verify all the business is done for release
     ~/kent/src/hg/utils/automation/verifyBrowser.pl canFam6
 # 71 tables in database canFam6 - Dog, Canis lupus familiaris
 # verified 60 tables in database canFam6, 11 extra tables, 19 optional tables
 # Ensembl genes 5 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     chainMm39       - extra table
 # 2     chainMm39Link   - extra table
 # 3     chainRBestMm39  - extra table
 # 4     chainRBestMm39Link      - extra table
 # . . . etc . . .
 # 8     crisprAllTargets        - extra table
 # 9     netMm39 - extra table
 # 10    netRBestMm39    - extra table
 # 11    netSynMm39      - extra table
 # 13 genbank tables found
 # verified 28 required tables, 1 missing tables
 # 1     ucscToRefSeq    - missing table
 # hg38 chainNet to canFam6 found 3 required tables
 # mm10 chainNet to canFam6 found 3 required tables
 # hg38 chainNet RBest and syntenic to canFam6 found 6 optional tables
 # mm10 chainNet RBest and syntenic to canFam6 found 3 optional tables
 # liftOver to previous versions: 2, from previous versions: 2
 # blatServers: canFam6 blat1b 17907 0 1 canFam6 blat1b 17906 1 0
 
     # fixup all.joiner until this is a clean output
     joinerCheck -database=canFam6 -tableCoverage all.joiner
     joinerCheck -database=canFam6 -times all.joiner
     joinerCheck -database=canFam6 -keys all.joiner
 
     # when clean, check in:
     git commit -m 'adding rules for canFam6 refs #27546' 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/canFam6
     time (makeDownloads.pl canFam6) > downloads.log 2>&1
     #  real    16m39.750s
 
     #   now ready for pushQ entry
     mkdir /hive/data/genomes/canFam6/pushQ
     cd /hive/data/genomes/canFam6/pushQ
  time ($HOME/kent/src/hg/utils/automation/makePushQSql.pl -redmineList canFam6) > canFam6.pushQ.sql 2> stderr.out
 XXX - running - Mon May 24 11:47:51 PDT 2021
     # real    15m12.083s
 
     # remove the tandemDups and gapOverlap from the file list:
     sed -i -e "/tandemDups/d" redmine.canFam6.table.list
     sed -i -e "/Tandem Dups/d" redmine.canFam6.releaseLog.txt
     sed -i -e "/gapOverlap/d" redmine.canFam6.table.list
     sed -i -e "/Gap Overlaps/d" redmine.canFam6.releaseLog.txt
 
     #   check for errors in stderr.out, some are OK, e.g.:
   # WARNING: canFam6 does not have seq
   # WARNING: canFam6 does not have extFile
 
     # verify the file list does correctly match to files
     cat redmine.canFam6.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.canFam6.table.list
     # 63 redmine.canFam6.table.list
 
     # how many actual:
     awk -F'.' '{printf "hgsql -N %s -e '"'"'show table status like \"%s\";'"'"'\n", $1, $2}' redmine.canFam6.table.list | sh | wc -l
     # 63
 
     # 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/canFam6/pushQ/redmine.canFam6.file.list
 #	/hive/data/genomes/canFam6/pushQ/redmine.canFam6.releaseLog.txt
 #	/hive/data/genomes/canFam6/pushQ/redmine.canFam6.table.list
 
-#########################################################################
+##############################################################################
+# LIFTOVER TO canFam2 (DONE - 2022-12-07 - Hiram)
+    ssh hgwdev
+    mkdir /hive/data/genomes/canFam6/bed/blat.canFam2.2022-12-07
+    cd /hive/data/genomes/canFam6/bed/blat.canFam2.2022-12-07
+    doSameSpeciesLiftOver.pl -verbose=2 \
+        -debug -bigClusterHub=ku -dbHost=hgwdev -workhorse=hgwdev \
+        -target2Bit=/hive/data/genomes/canFam6/canFam6.2bit \
+        -targetSizes=/hive/data/genomes/canFam6/chrom.sizes \
+        -query2Bit=/hive/data/genomes/canFam2/canFam2.2bit \
+        -querySizes=/hive/data/genomes/canFam2/chrom.sizes \
+        -ooc=/hive/data/genomes/canFam6/jkStuff/canFam6.11.ooc \
+         canFam6 canFam2
+    time (doSameSpeciesLiftOver.pl -verbose=2 \
+        -bigClusterHub=ku -dbHost=hgwdev -workhorse=hgwdev \
+        -target2Bit=/hive/data/genomes/canFam6/canFam6.2bit \
+        -targetSizes=/hive/data/genomes/canFam6/chrom.sizes \
+        -query2Bit=/hive/data/genomes/canFam2/canFam2.2bit \
+        -querySizes=/hive/data/genomes/canFam2/chrom.sizes \
+        -ooc=/hive/data/genomes/canFam6/jkStuff/canFam6.11.ooc \
+         canFam6 canFam2) > doLiftOverToCanFam2.log 2>&1
+    # real    2179m29.114s
+
+    # see if the liftOver menus function in the browser from canFam6 to canFam2
+
+##############################################################################