# for emacs: -*- mode: sh; -*- # This file describes browser build for the equCab3 ######################################################################### # reuse photograph from equCab2 previous versions # (DONE - 2018-04-03 - Hiram) mkdir /hive/data/genomes/equCab3 cd /hive/data/genomes/equCab3 cp -p ../equCab2/photoReference.txt . cat photoReference.txt photoCreditURL http://www.genome.gov/dmd/img.cfm?node=Photos/Animals/Horse&id=79086 photoCreditName NHGRI press photos ######################################################################### # Initial steps (DONE - 2018-04-03 - Hiram) # To start this initialBuild.txt document, from a previous assembly document: mkdir ~/kent/src/hg/makeDb/doc/equCab3 cd ~/kent/src/hg/makeDb/doc/equCab3 # best to use a most recent document since it has the latest features and # procedures: sed -e 's/panTro6/equCab3/g; s/PanTro6/EquCab3/g; s/DONE/TBD/g;' ../panTro6/initialBuild.txt > initialBuild.txt mkdir /hive/data/genomes/equCab3/refseq cd /hive/data/genomes/equCab3/refseq time rsync -L -a -P \ rsync://ftp.ncbi.nlm.nih.gov/genomes/refseq/vertebrate_mammalian/Equus_caballus/all_assembly_versions/GCF_002863925.1_EquCab3.0/ ./ # sent 3683 bytes received 3757064597 bytes 12544468.38 bytes/sec # total size is 3756592842 speedup is 1.00 # real 4m59.002s # check assembly size for later reference: faSize G*.0_genomic.fna.gz # 2506966135 bases (9435481 N's 2497530654 real 1761185522 upper # 736345132 lower) in 4701 sequences in 1 files # Total size: mean 533283.6 sd 6827354.4 min 2669 (NW_019642362.1) # max 188260577 (NC_009144.3) median 6592 # %29.37 masked total, %29.48 masked real # this information is from the top of # equCab3/refseq/GCF_002863925.1_EquCab3.0_assembly_report.txt # Assembly name: EquCab3.0 # Organism name: Equus caballus (horse) # Infraspecific name: breed=thoroughbred # Isolate: Twilight # Sex: female # Taxid: 9796 # BioSample: SAMN02953672 # BioProject: PRJNA421018 # Submitter: University of Louisville # Date: 2018-1-5 # Assembly type: haploid # Release type: major # Assembly level: Chromosome # Genome representation: full # WGS project: PJAA01 # Assembly method: Celera Assembler v. 2017; HiRise v. 2017 # Expected final version: yes # Reference guided assembly: de-novo # Genome coverage: 88.0x # Sequencing technology: Sanger; Illumina HiSeq; PacBio # RefSeq category: Representative Genome # GenBank assembly accession: GCA_002863925.1 # RefSeq assembly accession: GCF_002863925.1 # RefSeq assembly and GenBank assemblies identical: no # ## Assembly-Units: ## GenBank Unit Accession RefSeq Unit Accession Assembly-Unit name ## GCA_002863935.1 GCF_002863935.1 Primary Assembly ## GCF_000215765.1 non-nuclear ############################################################################# # establish config.ra file (DONE - Hiram - 2018-04-03) # arguments here are: cd /hive/data/genomes/equCab3 $HOME/kent/src/hg/utils/automation/prepConfig.pl equCab3 mammal \ horse ./refseq/*_assembly_report.txt > equCab3.config.ra # compare to ../equCab2 to see what might need to be fixed up: diff equCab3.config.ra ../equCab2/equCab2.config.ra | less # note, equCab2 is quite old and doesn't match well at all # verify it looks sane cat equCab3.config.ra # config parameters for makeGenomeDb.pl: db equCab3 clade mammal scientificName Equus caballus commonName Horse assemblyDate Jan. 2018 assemblyLabel University of Louisville assemblyShortLabel EquCab3.0 orderKey 8683 # mitochondrial sequence included in refseq release # mitoAcc NC_001640.1 mitoAcc none fastaFiles /hive/data/genomes/equCab3/ucsc/*.fa.gz agpFiles /hive/data/genomes/equCab3/ucsc/*.agp # qualFiles none dbDbSpeciesDir horse photoCreditURL http://www.genome.gov/dmd/img.cfm?node=Photos/Animals/Horse&id=79086 photoCreditName NHGRI press photos ncbiGenomeId 145 ncbiAssemblyId 1512011 ncbiAssemblyName EquCab3.0 ncbiBioProject 421018 ncbiBioSample SAMN02953672 genBankAccessionID GCF_002863925.1 taxId 9796 ############################################################################# # setup UCSC named files (DONE - 2018-05-23 - Hiram) # NOTE: new procedure here to manage these unmarked gaps # required changes to hgFakeAgp program mkdir /hive/data/genomes/equCab3/ucsc cd /hive/data/genomes/equCab3/ucsc # check for duplicate sequences: time faToTwoBit -noMask ../refseq/G*.0_genomic.fna.gz refseq.2bit # real 1m1.796s 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 # unfortunately the gaps are not annotated in this assembly # will construct a fake agp below time ~/kent/src/hg/utils/automation/ucscCompositeAgp.pl \ ../refseq/G*.0_genomic.fna.gz \ ../refseq/G*.0_assembly_structure/Primary_Assembly # NC_009144.3 chr1 # NC_009145.3 chr2 # NC_009146.3 chr3 # NC_009147.3 chr4 # NC_009148.3 chr5 # NC_009149.3 chr6 # NC_009150.3 chr7 # NC_009151.3 chr8 # NC_009152.3 chr9 # NC_009153.3 chr10 # NC_009154.3 chr11 # NC_009155.3 chr12 # NC_009156.3 chr13 # NC_009157.3 chr14 # NC_009158.3 chr15 # NC_009159.3 chr16 # NC_009160.3 chr17 # NC_009161.3 chr18 # NC_009162.3 chr19 # NC_009163.3 chr20 # NC_009164.3 chr21 # NC_009165.3 chr22 # NC_009166.3 chr23 # NC_009167.3 chr24 # NC_009168.3 chr25 # NC_009169.3 chr26 # NC_009170.3 chr27 # NC_009171.3 chr28 # NC_009172.3 chr29 # NC_009173.3 chr30 # NC_009174.3 chr31 # NC_009175.3 chrX # real 14m26.256s # unplaced sequences time ~/kent/src/hg/utils/automation/unplacedWithChroms.pl \ ../refseq/*_assembly_structure/Primary_Assembly # processed 4668 sequences into chrUn.fa.gz # real 0m43.355s # there are no unlocalized sequences time ~/kent/src/hg/utils/automation/unlocalizedWithChroms.pl \ ../refseq/*_assembly_structure/Primary_Assembly # bash syntax here mitoAcc=`grep "^# mitoAcc" ../equCab3.config.ra | awk '{print $NF}'` printf "# mitoAcc %s\n" "$mitoAcc" # mitoAcc NC_001640.1 zcat \ ../refseq/*_assembly_structure/non-nuclear/assem*/AGP/chrMT.comp.agp.gz \ | grep -v "^#" | sed -e "s/^$mitoAcc/chrM/;" > chrM.agp printf ">chrM\n" > chrM.fa twoBitToFa -noMask refseq.2bit:$mitoAcc stdout | grep -v "^>" >> chrM.fa gzip chrM.fa # the agp's constructed above were useless with no gaps rm -f *.agp # create a fake agp to annotate gaps, added new argument to hgFakeAgp # to better name these things:: hgFakeAgp -singleContigs -minContigGap=1 \ ../refseq/GCF_002863925.1_EquCab3.0_genomic.fna.gz refseq.fake.agp # need to fix up the names to ucsc names: grep -v "^#" \ ../refseq/GCF_002863925.1_EquCab3.0_assembly_structure/Primary_Assembly/assembled_chromosomes/chr2acc \ | awk '{printf "s/^%s/chr%s/;\n", $2, $1}' > refseqToUcsc.sed # this will maintain the contig names for chrUn from that AGP file zcat ../refseq/GCF_002863925.1_EquCab3.0_assembly_structure/Primary_Assembly/unplaced_scaffolds/AGP/unplaced.scaf.agp.gz \ | grep -v "^#" | awk '{printf "s/\\t%s/\\t%s/;\n", $1,$6}' \ > chrUnContigs.sed cat refseq.fake.agp | sed -f refseqToUcsc.sed \ | sed -e 's/^NW_\([0-9]\+\).\([0-9]\+\)/chrUn_NW_\1v\2/;' \ | sed -e 's/^NC_[0-9]\+.[0-9]\+/chrM/;' \ | sed -f chrUnContigs.sed > equCab3.ucsc.agp # verify this agp will match the fasta time faToTwoBit *.fa.gz test.2bit # real 1m10.237s checkAgpAndFa equCab3.ucsc.agp test.2bit 2>&1 | tail -4 # All AGP and FASTA entries agree - both files are valid # real 0m8.925s # and no sequence lost from orginal: twoBitToFa test.2bit stdout | faSize stdin # 2506966135 bases (9435481 N's 2497530654 real 2497530654 upper 0 lower) # in 4701 sequences in 1 files # Total size: mean 533283.6 sd 6827354.4 min 2669 (chrUn_NW_019642362v1) # max 188260577 (chr1) median 6592 # same numbers as above # 2506966135 bases (9435481 N's 2497530654 real 1761185522 upper # 736345132 lower) in 4701 sequences in 1 files # Total size: mean 533283.6 sd 6827354.4 min 2669 (NW_019642362.1) # max 188260577 (NC_009144.3) median 6592 # no longer need these temporary 2bit files rm refseq.2bit test.2bit ############################################################################# # Initial database build (DONE - 2018-05-23 - Hiram) cd /hive/data/genomes/equCab3 # verify sequence and AGP are OK: time (makeGenomeDb.pl -workhorse=hgwdev -dbHost=hgwdev -fileServer=hgwdev \ -stop=agp equCab3.config.ra) > agp.log 2>&1 # real 2m21.544s # verify there was no error in that step: tail agp.log # *** All done! (through the 'agp' step) # then finish it off: time (makeGenomeDb.pl -workhorse=hgwdev -dbHost=hgwdev \ -fileServer=hgwdev -continue=db equCab3.config.ra) > db.log 2>&1 # real 20m46.511s # verify gaps are all there: twoBitInfo -nBed equCab3.unmasked.2bit stdout | awk '{print $3-$2}' \ | ave stdin | sed -e 's/^/# /;' # Q1 20.000000 # median 1000.000000 # Q3 2172.000000 # average 1499.123133 # min 1.000000 # max 34650.000000 # count 6294 # total 9435481.000000 # standard deviation 2806.197972 hgsql -e 'select chromEnd-chromStart from gap;' equCab3 | ave stdin | sed -e 's/^/# /;' # Q1 20.000000 # median 1000.000000 # Q3 2172.000000 # average 1499.123133 # min 1.000000 # max 34650.000000 # count 6294 # total 9435481.000000 # standard deviation 2806.197972 # check in the trackDb files created in TemporaryTrackDbCheckout/ # and add equCab3 to trackDb/makefile # temporary symlink until masked sequence is available cd /hive/data/genomes/equCab3 ln -s `pwd`/equCab3.unmasked.2bit /gbdb/equCab3/equCab3.2bit ############################################################################## # cpgIslands on UNMASKED sequence (DONE - 2018-05-23 - Hiram) mkdir /hive/data/genomes/equCab3/bed/cpgIslandsUnmasked cd /hive/data/genomes/equCab3/bed/cpgIslandsUnmasked time (doCpgIslands.pl -dbHost=hgwdev -bigClusterHub=ku -buildDir=`pwd` \ -tableName=cpgIslandExtUnmasked \ -maskedSeq=/hive/data/genomes/equCab3/equCab3.unmasked.2bit \ -workhorse=hgwdev -smallClusterHub=ku equCab3) > do.log 2>&1 # real 5m36.146s cat fb.equCab3.cpgIslandExtUnmasked.txt # 43639817 bases of 2497530654 (1.747%) in intersection ############################################################################# # cytoBandIdeo - (DONE - 2018-05-23 - Hiram) mkdir /hive/data/genomes/equCab3/bed/cytoBand cd /hive/data/genomes/equCab3/bed/cytoBand makeCytoBandIdeo.csh equCab3 ############################################################################# # gapOverlap (DONE - 2018-05-23 - Hiram) mkdir /hive/data/genomes/equCab3/bed/gapOverlap cd /hive/data/genomes/equCab3/bed/gapOverlap time (doGapOverlap.pl \ -twoBit=/hive/data/genomes/equCab3/equCab3.unmasked.2bit equCab3 ) \ > do.log 2>&1 # real 2m49.728s cat fb.equCab3.gapOverlap.txt # 48566 bases of 2506966135 (0.002%) in intersection # only six items: zcat *.bed.gz | cut -f1-5 # chr12 113245358 113246724 chr12:113245359-113246724 633 # chr21 18867677 18869111 chr21:18867678-18869111 667 # chr8 127452459 127454559 chr8:127452460-127454559 1000 # chrX 52589209 52609380 chrX:52589210-52609380 1000 # chrY 7097196 7097619 chrY:7097197-7097619 199 ############################################################################# # tandemDups (DONE - 2018-05-23 - Hiram) mkdir /hive/data/genomes/equCab3/bed/tandemDups cd /hive/data/genomes/equCab3/bed/tandemDups time (~/kent/src/hg/utils/automation/doTandemDup.pl \ -twoBit=/hive/data/genomes/equCab3/equCab3.unmasked.2bit equCab3) \ > do.log 2>&1 & # real 108m30.433s cat fb.equCab3.tandemDups.txt # 26366982 bases of 2506966135 (1.052%) in intersection bigBedInfo equCab3.tandemDups.bb | sed -e 's/^/# /;' # version: 4 # fieldCount: 13 # hasHeaderExtension: yes # isCompressed: yes # isSwapped: 0 # extraIndexCount: 0 # itemCount: 354,039 # primaryDataSize: 9,521,689 # primaryIndexSize: 136,692 # zoomLevels: 9 # chromCount: 3648 # basesCovered: 449,107,941 # meanDepth (of bases covered): 5.195798 # minDepth: 1.000000 # maxDepth: 233.000000 # std of depth: 14.418242 ############################################################################# # run up idKeys files for chromAlias/ncbiRefSeq (DONE - 2018-05-23 - Hiram) # will need the refseq keys: mkdir /hive/data/genomes/equCab3/refseq/idKeys cd /hive/data/genomes/equCab3/refseq/idKeys faToTwoBit ../GCF_000001405.31_GRCh38.p5_genomic.fna.gz refseqEquCab3.2bit time (doIdKeys.pl \ -twoBit=`pwd`/refseqEquCab3.2bit \ -buildDir=`pwd` refseqEquCab3) > do.log 2>&1 & # real 3m23.365s cat refseqEquCab3.keySignature.txt # 9b81a6e3c94602c13436189783aadda8 # and the genbank keys: mkdir /hive/data/genomes/equCab3/refseq/idKeys/genbank cd /hive/data/genomes/equCab3/refseq/idKeys/genbank ln -s /hive/data/outside/ncbi/genomes/genbank/vertebrate_mammalian/Equus_caballus/all_assembly_versions/GCA_002863925.1_EquCab3.0/GCA_002863925.1_EquCab3.0_genomic.fna.gz . faToTwoBit GCA_002863925.1_EquCab3.0_genomic.fna.gz genbankEquCab3.2bit time (doIdKeys.pl \ -twoBit=`pwd`/genbankEquCab3.2bit \ -buildDir=`pwd` genbankEquCab3) > do.log 2>&1 & # real 3m25.325s cat genbankEquCab3.keySignature.txt # ea8c3522e6ac4dc1bec438c4f70043da # and the UCSC keys: mkdir /hive/data/genomes/equCab3/bed/idKeys cd /hive/data/genomes/equCab3/bed/idKeys time (doIdKeys.pl \ -twoBit=/hive/data/genomes/equCab3/equCab3.unmasked.2bit \ -buildDir=`pwd` equCab3) > do.log 2>&1 & # real 3m17.147s cat equCab3.keySignature.txt # 9b81a6e3c94602c13436189783aadda8 ############################################################################# # ucscToINSDC and ucscToRefSeq table/track (DONE - 2018-05-23 - 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/equCab3/bed/ucscToINSDC cd /hive/data/genomes/equCab3/bed/ucscToINSDC join -t$'\t' ../idKeys/equCab3.idKeys.txt \ ../../refseq/idKeys/genbank/genbankEquCab3.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/equCab3.idKeys.txt \ ../../refseq/idKeys/refseqEquCab3.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 # verify line counts are the same wc -l *.bed ../../chrom.sizes # 4700 ucscToINSDC.bed # 4701 ucscToRefSeq.bed # 4701 ../../chrom.sizes # need to find INSDC equivalents for chrM: egrep "chrM" * ucscToRefSeq.bed:chrM 0 16660 NC_001640.1 # lookup those accessions at NCBI Entrez # NC_001640.1 = X79547.1 printf "chrM\t0\t16660\tX79547.1\n" >> ucscToINSDC.bed # resort the bed file: sort -k1,1 -k2,2n -o ucscToINSDC.bed ucscToINSDC.bed # verify chrM is correct: egrep "chrM" * # ucscToINSDC.bed:chrM 0 16660 X79547.1 # ucscToRefSeq.bed:chrM 0 16660 NC_001640.1 # should be same line counts throughout: wc -l * ../../chrom.sizes # 4701 ucscToINSDC.bed # 4701 ucscToRefSeq.bed # 4701 ../../chrom.sizes export chrSize=`cut -f1 ucscToINSDC.bed | awk '{print length($0)}' | sort -n | tail -1` echo $chrSize # 27 # use the $chrSize in this sed sed -e "s/21/$chrSize/" $HOME/kent/src/hg/lib/ucscToINSDC.sql \ | hgLoadSqlTab equCab3 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 $chrSize # 20 sed -e "s/21/$chrSize/" $HOME/kent/src/hg/lib/ucscToINSDC.sql \ | sed -e 's/INSDC/RefSeq/g;' > ucscToRefSeq.sql hgLoadSqlTab equCab3 ucscToRefSeq ./ucscToRefSeq.sql ucscToRefSeq.bed # checkTableCoords should be silent checkTableCoords equCab3 # each should cover %100 entirely: featureBits -countGaps equCab3 ucscToINSDC # 2506966135 bases of 2506966135 (100.000%) in intersection featureBits -countGaps equCab3 ucscToRefSeq # 2506966135 bases of 2506966135 (100.000%) in intersection ######################################################################### # add chromAlias table (DONE - 2018-05-23 - Hiram) mkdir /hive/data/genomes/equCab3/bed/chromAlias cd /hive/data/genomes/equCab3/bed/chromAlias hgsql -N -e 'select chrom,name from ucscToRefSeq;' equCab3 \ | sort -k1,1 > ucsc.refseq.tab hgsql -N -e 'select chrom,name from ucscToINSDC;' equCab3 \ | sort -k1,1 > ucsc.genbank.tab ### Adding Ensembl alias with v95 release, after idKeys made: 2019-01-16 join -t$'\t' ../idKeys/equCab3.idKeys.txt \ ../../ens95/ensEquCab3.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, $3}' \ | sort -k1,1 -k2,2n > ucscToEns.bed cut -f1,4 ucscToEns.bed | sort > ucsc.ensembl.tab wc -l *.tab # 4701 ucsc.ensembl.tab # 4701 ucsc.genbank.tab # 4701 ucsc.refseq.tab ~/kent/src/hg/utils/automation/chromAlias.pl ucsc.*.tab \ > equCab3.chromAlias.tab for t in refseq genbank ensembl do c0=`cat ucsc.$t.tab | wc -l` c1=`grep $t equCab3.chromAlias.tab | wc -l` ok="OK" if [ "$c0" -ne "$c1" ]; then ok="ERROR" fi printf "# checking $t: $c0 =? $c1 $ok\n" done # checking refseq: 4701 =? 4701 OK # checking genbank: 4701 =? 4701 OK # checking ensembl: 4701 =? 4701 OK hgLoadSqlTab equCab3 chromAlias ~/kent/src/hg/lib/chromAlias.sql \ equCab3.chromAlias.tab ######################################################################### # fixup search rule for assembly track/gold table (DONE - 2018-05-23 - Hiram) cd ~/kent/src/hg/makeDb/trackDb/horse/equCab3 # preview prefixes and suffixes: hgsql -N -e "select frag from gold;" equCab3 \ | sed -e 's/[0-9][0-9]*//;' | sort | uniq -c | sed -e 's/^/#\t/;' # 1 NC_.1 # 32 NC_.3_1 # 32 NC_.3_10 # 16 NC_.3_100 # 14 NC_.3_101 # ... # 2985 PJAA.1 # 1683 PJAA.1_1 # 9 PJAA.1_10 # 8 PJAA.1_11 # 7 PJAA.1_12 # implies a rule: '[NP][CJ][A_][A0-9]+(\.[0-9]+[0-9_]*)?' # verify this rule will find them all and eliminate them all: hgsql -N -e "select frag from gold;" equCab3 | wc -l # 10995 hgsql -N -e "select frag from gold;" equCab3 \ | egrep -e '[NP][CJ][A_][A0-9]+(\.[0-9]+[0-9_]*)?' | wc -l # 10995 hgsql -N -e "select frag from gold;" equCab3 \ | egrep -v -e '[NP][CJ][A_][A0-9]+(\.[0-9]+[0-9_]*)?' | wc -l # 0 # hence, add to trackDb/chicken/equCab3/trackDb.ra searchTable gold shortCircuit 1 termRegex [NP][CJ][A_][A0-9]+(\.[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 - 2018-05-23 - Hiram) mkdir /hive/data/genomes/equCab3/bed/repeatMasker cd /hive/data/genomes/equCab3/bed/repeatMasker time (doRepeatMasker.pl -buildDir=`pwd` \ -bigClusterHub=ku -dbHost=hgwdev -workhorse=hgwdev \ -smallClusterHub=ku equCab3) > do.log 2>&1 & # real 827m18.308s egrep "bases|Total|masked" faSize.rmsk.txt \ | fold -w 75 -s | sed -e 's/^/# /;' # 2506966135 bases (9435481 N's 2497530654 real 1386909673 upper 1110620981 # lower) in 4701 sequences in 1 files # Total size: mean 533283.6 sd 6827354.4 min 2669 (chrUn_NW_019642362v1) max # 188260577 (chr1) median 6592 # %44.30 masked total, %44.47 masked real egrep -i "versi|relea" do.log # RepeatMasker version open-4.0.7 # February 01 2017 (open-4-0-7) 1.331 version of RepeatMasker # CC Dfam_Consensus RELEASE 20170127; * # CC RepBase RELEASE 20170127; * time featureBits -countGaps equCab3 rmsk # 1110729430 bases of 2506966135 (44.306%) in intersection # real 0m34.031s # 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;' equCab3 \ | bedSingleCover.pl stdin | ave -col=4 stdin | grep "^total" # total 1110729430.000000 # real 0m29.699s ########################################################################## # running simple repeat (DONE - 2018-05-23 - Hiram) mkdir /hive/data/genomes/equCab3/bed/simpleRepeat cd /hive/data/genomes/equCab3/bed/simpleRepeat # using trf409 6 here as similar size to genome (human == 6) time (doSimpleRepeat.pl -buildDir=`pwd` -bigClusterHub=ku \ -dbHost=hgwdev -workhorse=hgwdev -smallClusterHub=ku \ -trf409 6 equCab3) > do.log 2>&1 & # real 27m10.606s cat fb.simpleRepeat # 36058802 bases of 2497530654 (1.444%) in intersection bigBedInfo *.bb | sed -e 's/^/# /;' # version: 4 # fieldCount: 16 # hasHeaderExtension: yes # isCompressed: yes # isSwapped: 0 # extraIndexCount: 0 # itemCount: 395,037 # primaryDataSize: 13,549,643 # primaryIndexSize: 161,088 # zoomLevels: 10 # chromCount: 4141 # basesCovered: 36,058,802 # meanDepth (of bases covered): 1.649509 # minDepth: 1.000000 # maxDepth: 21.000000 # std of depth: 1.069993 # adding this trfMask to the other masking cd /hive/data/genomes/equCab3 # when using the Window Masker result: # twoBitMask bed/windowMasker/equCab3.cleanWMSdust.2bit \ # -add bed/simpleRepeat/trfMask.bed equCab3.2bit # you can safely ignore the warning about fields >= 13 # when using Rmsk results, add to rmsk after it is done: twoBitMask equCab3.rmsk.2bit \ -add bed/simpleRepeat/trfMask.bed equCab3.2bit # you can safely ignore the warning about fields >= 13 twoBitToFa equCab3.2bit stdout | faSize stdin > faSize.equCab3.2bit.txt egrep "bases|Total|masked" faSize.equCab3.2bit.txt \ | fold -w 75 -s | sed -e 's/^/# /;' # 2506966135 bases (9435481 N's 2497530654 real 1386367759 upper 1111162895 # lower) in 4701 sequences in 1 files # Total size: mean 533283.6 sd 6827354.4 min 2669 (chrUn_NW_019642362v1) max # 188260577 (chr1) median 6592 # %44.32 masked total, %44.49 masked real # reset the symlink rm /gbdb/equCab3/equCab3.2bit ln -s `pwd`/equCab3.2bit /gbdb/equCab3/equCab3.2bit ######################################################################### # CREATE MICROSAT TRACK (DONE - 2018-05-24 - Hiram) ssh hgwdev mkdir /cluster/data/equCab3/bed/microsat cd /cluster/data/equCab3/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 equCab3 microsat microsat.bed # Read 10322 elements of size 4 from microsat.bed ########################################################################## ## WINDOWMASKER (DONE - 2018-05-23 - Hiram) mkdir /hive/data/genomes/equCab3/bed/windowMasker cd /hive/data/genomes/equCab3/bed/windowMasker time (doWindowMasker.pl -buildDir=`pwd` -workhorse=hgwdev \ -dbHost=hgwdev equCab3) > do.log 2>&1 # real 188m5.912s # Masking statistics cat faSize.equCab3.cleanWMSdust.txt egrep "bases|Total|masked" faSize.equCab3.cleanWMSdust.txt \ | fold -w 75 -s | sed -e 's/^/# /;' # 3050398082 bases (31805092 N's 3018592990 real 1812556664 upper 1206036326 # lower) in 4346 sequences in 1 files # Total size: mean 701886.4 sd 9434013.2 min 223 (chrUn_NW_019937062v1) max # 224244399 (chr1) median 29187 # %39.54 masked total, %39.95 masked real cat fb.equCab3.rmsk.windowmaskerSdust.txt # 519201765 bases of 2506966135 (20.710%) in intersection # since this was run at the same time of RM, failed at the end # of the load step with the featureBits measurement, therefore # continue with cleanup: time (doWindowMasker.pl -buildDir=`pwd` -workhorse=hgwdev \ -continue=cleanup -dbHost=hgwdev equCab3) > cleanup.log 2>&1 # real 1m59.683s ############################################################################# # ncbiRefSeq (TBD - 2018-03-24 - Hiram) # can be run up after ucscToRefSeq table is constructed mkdir /hive/data/genomes/equCab3/bed/ncbiRefSeq cd /hive/data/genomes/equCab3/bed/ncbiRefSeq # adjust the name arguments time (~/kent/src/hg/utils/automation/doNcbiRefSeq.pl -buildDir=`pwd` \ -bigClusterHub=ku -dbHost=hgwdev \ -fileServer=hgwdev -smallClusterHub=ku -workhorse=hgwdev \ refseq vertebrate_mammalian Pan_troglodytes \ GCF_002880755.1_Clint_0 equCab3) > do.log 2>&1 # real 10m2.131s # started this too early. It needs to run after the equCab3.2bit file # has been masked. Rerunning from process step: time (~/kent/src/hg/utils/automation/doNcbiRefSeq.pl -buildDir=`pwd` \ -continue=process -bigClusterHub=ku -dbHost=hgwdev \ -fileServer=hgwdev -smallClusterHub=ku -workhorse=hgwdev \ refseq vertebrate_mammalian Pan_troglodytes \ GCF_002880755.1_Clint_0 equCab3) > process.log 2>&1 & # real 8m52.047s cat fb.ncbiRefSeq.equCab3.txt # 81659062 bases of 2476453204 (3.297%) in intersection ############################################################################# # cpgIslands - (DONE - 2018-05-24 - Hiram) mkdir /hive/data/genomes/equCab3/bed/cpgIslands cd /hive/data/genomes/equCab3/bed/cpgIslands time (doCpgIslands.pl -dbHost=hgwdev -bigClusterHub=ku \ -workhorse=hgwdev -smallClusterHub=ku equCab3) > do.log 2>&1 & # real 6m39.343s cat fb.equCab3.cpgIslandExt.txt # 27798148 bases of 2497530654 (1.113%) in intersection ############################################################################## # genscan - (DONE - 2018-05-24 - Hiram) mkdir /hive/data/genomes/equCab3/bed/genscan cd /hive/data/genomes/equCab3/bed/genscan time (doGenscan.pl -buildDir=`pwd` -workhorse=hgwdev -dbHost=hgwdev \ -bigClusterHub=ku equCab3) > do.log 2>&1 & # real 61m35.362s # two broken jobs run with window size 2,000,000 to complete # real 69m43.551s time (doGenscan.pl -buildDir=`pwd` -workhorse=hgwdev -dbHost=hgwdev \ -continue=makeBed -bigClusterHub=ku equCab3) > makeBed.log 2>&1 & # real 1m20.373s cat fb.equCab3.genscan.txt # 57690912 bases of 2497530654 (2.310%) in intersection cat fb.equCab3.genscanSubopt.txt # 53358129 bases of 2497530654 (2.136%) in intersection bigBedInfo equCab3.genscan.bb | sed -e 's/^/# /;' # version: 4 # fieldCount: 12 # hasHeaderExtension: yes # isCompressed: yes # isSwapped: 0 # extraIndexCount: 0 # itemCount: 45,631 # primaryDataSize: 2,718,247 # primaryIndexSize: 53,748 # zoomLevels: 8 # chromCount: 1263 # basesCovered: 1,755,228,037 # meanDepth (of bases covered): 1.000000 # minDepth: 1.000000 # maxDepth: 1.000000 # std of depth: -nan ############################################################################# # augustus gene track (DONE - 2018-05-24 - Hiram) mkdir /hive/data/genomes/equCab3/bed/augustus cd /hive/data/genomes/equCab3/bed/augustus time (doAugustus.pl -buildDir=`pwd` -bigClusterHub=ku \ -species=human -dbHost=hgwdev -workhorse=hgwdev equCab3) > do.log 2>&1 & # real 128m42.217s cat fb.equCab3.augustusGene.txt # 53699750 bases of 2497530654 (2.150%) in intersection bigBedInfo equCab3.augustus.bb | sed -e 's/^/# /;' # version: 4 # fieldCount: 20 # hasHeaderExtension: yes # isCompressed: yes # isSwapped: 0 # extraIndexCount: 0 # itemCount: 31,777 # primaryDataSize: 2,271,720 # primaryIndexSize: 28,912 # zoomLevels: 7 # chromCount: 490 # basesCovered: 1,282,501,964 # meanDepth (of bases covered): 1.249708 # minDepth: 1.000000 # maxDepth: 5.000000 # std of depth: 0.619201 ############################################################################# # lastz/chain/net swap human/hg38 (DONE - 2018-05-25 - Hiram) # original alignment cd /hive/data/genomes/hg38/bed/lastzEquCab3.2018-05-25 cat fb.hg38.chainEquCab3Link.txt # 1705190736 bases of 3049335806 (55.920%) in intersection cat fb.hg38.chainSynEquCab3Link.txt # 1642798373 bases of 3049335806 (53.874%) in intersection cat fb.hg38.chainRBest.EquCab3.txt # 1563820848 bases of 3049335806 (51.284%) in intersection # and for the swap: mkdir /hive/data/genomes/equCab3/bed/blastz.hg38.swap cd /hive/data/genomes/equCab3/bed/blastz.hg38.swap time (doBlastzChainNet.pl -verbose=2 \ /hive/data/genomes/hg38/bed/lastzEquCab3.2018-05-25/DEF \ -swap -chainMinScore=3000 -chainLinearGap=medium \ -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \ -syntenicNet) > swap.log 2>&1 & # real 122m26.771s cat fb.equCab3.chainHg38Link.txt # 1666879638 bases of 2497530654 (66.741%) in intersection cat fb.equCab3.chainSynHg38Link.txt # 1624977128 bases of 2497530654 (65.063%) in intersection time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` equCab3 hg38) > rbest.log 2>&1 & # real 473m11.347s cat fb.equCab3.chainRBest.Hg38.txt # 1563886386 bases of 2497530654 (62.617%) in intersection ############################################################################# # lastz/chain/net swap mouse/mm10 (DONE - 2018-05-25 - Hiram) # alignment to mouse/mm10: cd /hive/data/genomes/mm10/bed/lastzEquCab3.2018-05-25 cat fb.mm10.chainEquCab3Link.txt # 921489718 bases of 2652783500 (34.737%) in intersection cat fb.mm10.chainSynEquCab3Link.txt # 876836391 bases of 2652783500 (33.053%) in intersection cat fb.mm10.chainRBest.EquCab3.txt # 876785778 bases of 2652783500 (33.052%) in intersection # and for the swap: mkdir /hive/data/genomes/equCab3/bed/blastz.mm10.swap cd /hive/data/genomes/equCab3/bed/blastz.mm10.swap time (doBlastzChainNet.pl -verbose=2 \ /hive/data/genomes/mm10/bed/lastzEquCab3.2018-05-25/DEF \ -swap -chainMinScore=3000 -chainLinearGap=medium \ -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \ -syntenicNet) > swap.log 2>&1 & # real 83m14.250s cat fb.equCab3.chainMm10Link.txt # 930516778 bases of 2497530654 (37.257%) in intersection cat fb.equCab3.chainSynMm10Link.txt # 897238830 bases of 2497530654 (35.925%) in intersection time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` equCab3 mm10) > rbest.log 2>&1 & # real 318m40.520s cat fb.equCab3.chainRBest.Mm10.txt # 875954606 bases of 2497530654 (35.073%) in intersection ############################################################################## # Create kluster run files (DONE - 2018-05-25 - Hiram) cd /hive/data/genomes/equCab3 # numerator is equCab3 gapless bases "real" as reported by: featureBits -noRandom -noHap equCab3 gap # 3324287 bases of 2405835607 (0.138%) 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 \( 2405835607 / 2861349177 \) \* 1024 # ( 2405835607 / 2861349177 ) * 1024 = 860.983931 # ==> use -repMatch=800, was 825 equCab2 cd /hive/data/genomes/equCab3 blat equCab3.2bit \ /dev/null /dev/null -tileSize=11 -makeOoc=jkStuff/equCab3.11.ooc \ -repMatch=800 # Wrote 29317 overused 11-mers to jkStuff/equCab3.11.ooc # equCab2 at repMatch=825 was: # Wrote 25375 overused 11-mers to equCab2.11.ooc # There are no non-bridged gaps in this assembly # check non-bridged gaps to see what the typical size is: hgsql -N \ -e 'select * from gap where bridge="no" order by size;' equCab3 \ | sort -k7,7nr | ave -col=7 stdin | sed -e 's/^/# /;' # there are many at 100 bases: # Q1 100.000000 # median 100.000000 # Q3 100.000000 # average 10930.290698 # min 10.000000 # max 500001.000000 # count 86 # total 940005.000000 # standard deviation 56419.602180 # profile: hgsql -N -e 'select * from gap where bridge="no" order by size;' equCab3 \ | cut -f7 | sort | uniq -c 1 10 74 100 1 10223 1 131931 1 15585 1 29588 1 32403 1 33521 1 500001 2 50001 1 70431 1 8910 # therefore, minimum gap size of 100, this is doing non-bridged gaps only gapToLift -verbose=2 -minGap=100 equCab3 jkStuff/equCab3.nonBridged.lft \ -bedFile=stdout | sort -k1,1 -k2,2n > jkStuff/equCab3.nonBridged.bed ############################################################################## # LIFTOVER TO equCab2 (DONE - 2018-05-25 - Hiram) ssh hgwdev mkdir /hive/data/genomes/equCab3/bed/blat.equCab2.2018-05-25 cd /hive/data/genomes/equCab3/bed/blat.equCab2.2018-05-25 time (doSameSpeciesLiftOver.pl -verbose=2 -buildDir=`pwd` \ -ooc=/hive/data/genomes/equCab3/jkStuff/equCab3.11.ooc \ -bigClusterHub=ku -dbHost=hgwdev -workhorse=hgwdev \ equCab3 equCab2) > do.log 2>&1 # real 439m22.186s # verify the convert link on the test browser is now active from equCab3 to # equCab2 ############################################################################## # GENBANK AUTO UPDATE (DONE - 2018-03-25 - Hiram) ssh hgwdev cd $HOME/kent/src/hg/makeDb/genbank git pull # /cluster/data/genbank/data/organism.lst shows: # #organism mrnaCnt estCnt refSeqCnt # Equus caballus 29381 37758 1146 # edit etc/genbank.conf to add equCab3 just before equCab2 # equCab3 (Equus caballus) equCab3.serverGenome = /hive/data/genomes/equCab3/equCab3.2bit equCab3.clusterGenome = /scratch/data/equCab3/equCab3.2bit equCab3.ooc = /hive/data/genomes/equCab3/jkStuff/equCab3.11.ooc equCab3.lift = no equCab3.downloadDir = equCab3 equCab3.refseq.mrna.native.pslCDnaFilter = ${ordered.refseq.mrna.native.pslCDnaFilter} equCab3.refseq.mrna.xeno.pslCDnaFilter = ${ordered.refseq.mrna.xeno.pslCDnaFilter} equCab3.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter} equCab3.genbank.mrna.xeno.pslCDnaFilter = ${ordered.genbank.mrna.xeno.pslCDnaFilter} equCab3.genbank.est.native.pslCDnaFilter = ${ordered.genbank.est.native.pslCDnaFilter} # defaults yes: genbank.mrna.native.load genbank.mrna.native.loadDesc # yes: genbank.est.native.load refseq.mrna.native.load # yes: refseq.mrna.native.loadDesc refseq.mrna.xeno.load # yes: refseq.mrna.xeno.loadDesc # defaults no: genbank.mrna.xeno.load genbank.mrna.xeno.loadDesc # no: genbank.est.native.loadDesc genbank.est.xeno.load # no: genbank.est.xeno.loadDesc # DO NOT NEED genbank.mrna.xeno except for human, mouse # equCab3.upstreamGeneTbl = refGene # equCab3.upstreamMaf = multiz6way /hive/data/genomes/equCab3/bed/multiz6way/species.list # verify stated file paths do exist: grep equCab3 etc/genbank.conf | egrep "Genome|ooc|lift" \ | awk '{print $NF}' | grep -v -w no | xargs ls -og -rw-rw-r-- 1 653547323 May 24 16:07 /hive/data/genomes/equCab3/equCab3.2bit -rw-rw-r-- 1 653547323 May 24 16:07 /hive/data/genomes/equCab3/equCab3.2bit -rw-rw-r-- 1 117276 May 25 09:33 /hive/data/genomes/equCab3/jkStuff/equCab3.11.ooc # add equCab3 to: # etc/align.dbs etc/hgwdev.dbs git commit -m 'adding equCab3/horse refs #21223' \ etc/genbank.conf etc/align.dbs etc/hgwdev.dbs git push # update /cluster/data/genbank/: make etc-update # XXX a few days later the genbank tables will be in the database ############################################################################# # BLATSERVERS ENTRY (DONE - 2018-05-29 - 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 ("equCab3", "blat1d", "17900", "1", "0"); \ INSERT INTO blatServers (db, host, port, isTrans, canPcr) \ VALUES ("equCab3", "blat1d", "17901", "0", "1");' \ hgcentraltest # test it with some sequence ############################################################################## ## reset default position to same as what equCab2 has ## (DONE - 2018-05-29 - Hiram) ssh hgwdev hgsql -e 'update dbDb set defaultPos="chr11:53320263-53382039" where name="equCab3";' hgcentraltest ############################################################################## # all.joiner update, downloads and in pushQ - (DONE - 2018-06-11 - Hiram) cd $HOME/kent/src/hg/makeDb/schema ~/kent/src/hg/utils/automation/verifyBrowser.pl equCab3 # 56 tables in database equCab3 - Horse, Equus caballus # verified 55 tables in database equCab3, 1 extra tables, 14 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 splitOverlap - extra table # 12 genbank tables found # verified 29 required tables, 0 missing tables # hg38 chainNet to equCab3 found 3 required tables # mm10 chainNet to equCab3 found 3 required tables # hg38 chainNet RBest and syntenic to equCab3 found 6 optional tables # mm10 chainNet RBest and syntenic to equCab3 found 3 optional tables # liftOver to previous versions: 1, from previous versions: 1 # fixup all.joiner until this is a clean output joinerCheck -database=equCab3 -tableCoverage all.joiner joinerCheck -database=equCab3 -times all.joiner joinerCheck -database=equCab3 -keys all.joiner cd /hive/data/genomes/equCab3 rm -fr TemporaryTrackDbCheckout time (makeDownloads.pl -workhorse=hgwdev equCab3) > downloads.log 2>&1 # real 23m53.926s # now ready for pushQ entry mkdir /hive/data/genomes/equCab3/pushQ cd /hive/data/genomes/equCab3/pushQ time (makePushQSql.pl -redmineList equCab3) > equCab3.pushQ.sql 2> stderr.out XXX - running - Mon Jun 11 15:32:33 PDT 2018 # real 4m3.493s # remove the tandemDups and gapOverlaps from the file list: sed -i -e "/tandemDups/d" redmine.equCab3.table.list sed -i -e "/Tandem Dups/d" redmine.equCab3.releaseLog.txt sed -i -e "/gapOverlap/d" redmine.equCab3.table.list sed -i -e "/Gap Overlaps/d" redmine.equCab3.releaseLog.txt # check for errors in stderr.out, some are OK, e.g.: # WARNING: equCab3 does not have seq # WARNING: equCab3 does not have extFile # add the path names to the listing files in the redmine issue # in the three appropriate entry boxes: /hive/data/genomes/equCab3/pushQ/redmine.equCab3.file.list /hive/data/genomes/equCab3/pushQ/redmine.equCab3.releaseLog.txt /hive/data/genomes/equCab3/pushQ/redmine.equCab3.table.list #########################################################################