# for emacs: -*- mode: sh; -*- # This file describes browser build for the papAnu3 ######################################################################### # reuse photograph from papAnu2 previous versions # (DONE - 2017-06-20 - Hiram) mkdir /hive/data/genomes/papAnu3 cd /hive/data/genomes/papAnu3 cp -p ../papAnu2/photoReference.txt . cat photoReference.txt photoCreditURL http://www.oumedicine.com/pathology/general-program-info/faculty-staff/roman-f-wolf-dvm photoCreditName Roman Wolf, University of Oklahoma Health Sciences Center ######################################################################### # Initial steps (DONE - 2017-06-20 - Hiram) # To start this initialBuild.txt document, from a previous assembly document: mkdir ~/kent/src/hg/makeDb/doc/papAnu3 cd ~/kent/src/hg/makeDb/doc/papAnu3 # best to use a most recent document since it has the latest features and # procedures: sed -e 's/xenTro9/papAnu3/g; s/XenTro9/PapAnu3/g; s/DONE/TBD/g;' ../xenTro9/initialBuild.txt > initialBuild.txt mkdir /hive/data/genomes/papAnu3/refseq cd /hive/data/genomes/papAnu3/refseq rsync -L -a -P \ rsync://ftp.ncbi.nlm.nih.gov/genomes/refseq/vertebrate_mammalian/Papio_anubis/all_assembly_versions/GCF_000264685.2_Panu_2.0/ ./ # sent 2600 bytes received 4190503044 bytes 10183488.81 bytes/sec # total size is 4189981785 speedup is 1.00 # check assembly size for later reference: faSize G*_2.0_genomic.fna.gz # 2948397226 bases (55130419 N's 2893266807 real 1783082117 upper # 1110184690 lower) in 63251 sequences in 1 files # Total size: mean 46614.2 sd 2497421.7 min 200 (NW_003880573.1) # max 220367699 (NC_018152.1) median 1416 # %37.65 masked total, %38.37 masked real # this information is from the top of # papAnu3/refseq/GCF_000264685.2_Panu_2.0_assembly_report.txt # Assembly name: Panu_2.0 # Organism name: Papio anubis (olive baboon) # Isolate: 1X1155 # Sex: female # Taxid: 9555 # BioSample: SAMN02981400 # BioProject: PRJNA169345 # Submitter: Baylor College of Medicine # Date: 2013-2-4 # Synonyms: papAnu2 # Assembly type: haploid # Release type: # Assembly level: Chromosome # Genome representation: full # WGS project: AHZZ01 # Assembly method: CABOG v. 6.1; ATLAS-LINK v. 1.0; ATLAS-GAPFILL v. 2.0 # Genome coverage: 2.5x Sanger; 4.5x 454; 85x Illumina # Sequencing technology: Sanger 3730; 454 FLX; Illumina # RefSeq category: Representative Genome # GenBank assembly accession: GCA_000264685.1 # RefSeq assembly accession: GCF_000264685.2 # RefSeq assembly and GenBank assemblies identical: no # ## Assembly-Units: ## GenBank Unit Accession RefSeq Unit Accession Assembly-Unit name ## GCA_000264695.1 GCF_000264695.1 Primary Assembly ## GCF_000749495.1 non-nuclear ############################################################################# # establish config.ra file (DONE - Hiram - 2017-06-20) # arguments here are: cd /hive/data/genomes/papAnu3 $HOME/kent/src/hg/utils/automation/prepConfig.pl papAnu3 vertebrate \ baboon ./refseq/*_assembly_report.txt > papAnu3.config.ra # fixup common name to remain compatible with previous panAnu2 version # and therfore orderKey wasn't correct. Also fixup shortLabel # to check orderKey: hgsql -e 'select name,orderKey,organism from dbDb order by orderKey;' \ hgcentraltest | less # verify it looks sane cat papAnu3.config.ra # config parameters for makeGenomeDb.pl: db papAnu3 clade vertebrate genomeCladePriority 70 scientificName Papio anubis commonName Baboon assemblyDate Feb. 2013 assemblyLabel Baylor College of Medicine assemblyShortLabel Baylor Panu_2.0 orderKey 2049 # mitochondrial sequence included in refseq release # mitoAcc NC_020006.2 mitoAcc none fastaFiles /hive/data/genomes/papAnu3/ucsc/*.fa.gz agpFiles /hive/data/genomes/papAnu3/ucsc/*.agp # qualFiles none dbDbSpeciesDir baboon photoCreditURL http://www.oumedicine.com/pathology/general-program-info/faculty-staff/roman-f-wolf-dvm photoCreditName Roman Wolf, University of Oklahoma Health Sciences Center ncbiGenomeId 394 ncbiAssemblyId 399268 ncbiAssemblyName Panu_2.0 ncbiBioProject 169345 ncbiBioSample SAMN02981400 genBankAccessionID GCF_000264685.2 taxId 9555 ############################################################################# # setup UCSC named files (DONE - 2017-06-20 - Hiram) mkdir /hive/data/genomes/papAnu3/ucsc cd /hive/data/genomes/papAnu3/ucsc # check for duplicate sequences: time faToTwoBit -noMask ../refseq/G*_2.0_genomic.fna.gz refseq.2bit # real 1m15.720s 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 ~/kent/src/hg/utils/automation/ucscCompositeAgp.pl \ ../refseq/G*_2.0_genomic.fna.gz \ ../refseq/G*_2.0_assembly_structure/Primary_Assembly # NC_018152.1 chr1 # NC_018153.1 chr2 # NC_018154.1 chr3 # NC_018155.1 chr4 # NC_018156.1 chr5 # NC_018157.1 chr6 # NC_018158.1 chr7 # NC_018159.1 chr8 # NC_018160.1 chr9 # NC_018161.1 chr10 # NC_018162.1 chr11 # NC_018163.1 chr12 # NC_018164.1 chr13 # NC_018165.1 chr14 # NC_018166.1 chr15 # NC_018167.1 chr16 # NC_018168.1 chr17 # NC_018169.1 chr18 # NC_018170.1 chr19 # NC_018171.1 chr20 # NC_018172.1 chrX time ~/kent/src/hg/utils/automation/unplacedWithChroms.pl \ ../refseq/*_assembly_structure/Primary_Assembly # processed 63229 sequences into chrUn.fa.gz # real 23m8.123s # there are no unlocalized sequences # time ~/kent/src/hg/utils/automation/unlocalizedWithChroms.pl \ # ../refseq/*_assembly_structure/Primary_Assembly # bash syntax here mitoAcc=`grep "^# mitoAcc" ../papAnu3.config.ra | awk '{print $NF}'` printf "# mitoAcc %s\n" "$mitoAcc" # mitoAcc NC_020006.2 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 # verify fasta and AGPs agree time faToTwoBit *.fa.gz test.2bit # real 1m20.981s time cat *.agp | checkAgpAndFa stdin test.2bit 2>&1 | tail -4 # All AGP and FASTA entries agree - both files are valid # real 0m44.106s # and no sequence lost from orginal: twoBitToFa test.2bit stdout | faSize stdin # 2948397226 bases (55130419 N's 2893266807 real 2893266807 upper 0 lower) # in 63251 sequences in 1 files # Total size: mean 46614.2 sd 2497421.7 min 200 (chrUn_NW_003880573v1) # max 220367699 (chr1) median 1416 # %0.00 masked total, %0.00 masked real # same numbers as above # 2948397226 bases (55130419 N's 2893266807 real 1783082117 upper # 1110184690 lower) in 63251 sequences in 1 files # Total size: mean 46614.2 sd 2497421.7 min 200 (NW_003880573.1) # max 220367699 (NC_018152.1) median 1416 # no longer need these temporary 2bit files rm refseq.2bit test.2bit ############################################################################# # Initial database build (DONE - 2017-06-20 - Hiram) cd /hive/data/genomes/papAnu3 # verify sequence and AGP are OK: time (makeGenomeDb.pl -workhorse=hgwdev -dbHost=hgwdev -fileServer=hgwdev \ -stop=agp papAnu3.config.ra) > agp.log 2>&1 # real 3m14.288s # 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 papAnu3.config.ra) > db.log 2>&1 # real 24m55.338s # check in the trackDb files created in TemporaryTrackDbCheckout/ # and add papAnu3 to trackDb/makefile # temporary symlink until masked sequence is available cd /hive/data/genomes/papAnu3 ln -s `pwd`/papAnu3.unmasked.2bit /gbdb/papAnu3/papAnu3.2bit ############################################################################## # cpgIslands on UNMASKED sequence (DONE - 2017-05-20 - Hiram) mkdir /hive/data/genomes/papAnu3/bed/cpgIslandsUnmasked cd /hive/data/genomes/papAnu3/bed/cpgIslandsUnmasked time (doCpgIslands.pl -dbHost=hgwdev -bigClusterHub=ku -buildDir=`pwd` \ -tableName=cpgIslandExtUnmasked \ -maskedSeq=/hive/data/genomes/papAnu3/papAnu3.unmasked.2bit \ -workhorse=hgwdev -smallClusterHub=ku papAnu3) > do.log 2>&1 # real 10m10.843s cat fb.papAnu3.cpgIslandExtUnmasked.txt # 39762268 bases of 2893270787 (1.374%) in intersection ############################################################################# # cytoBandIdeo - (DONE - 2017-06-20 - Hiram) mkdir /hive/data/genomes/papAnu3/bed/cytoBand cd /hive/data/genomes/papAnu3/bed/cytoBand makeCytoBandIdeo.csh papAnu3 ######################################################################### # ucscToINSDC and ucscToRefSeq table/track (DONE - 2017-06-20 - 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/papAnu3/bed/ucscToINSDC cd /hive/data/genomes/papAnu3/bed/ucscToINSDC # find accession for chrM grep chrM ../../papAnu3.agp # chrM 1 16516 1 O NC_020006.2 1 16516 + # find the genbank accession for NC_020006.2 at Entrez nucleotide # The NC_020006.2 name is the RefSeq name, the genbank name is: JX946196.2 # the assembly_report does not have this AY name since the chrM sequence # is not in the genbank assembly: grep NC_020006.2 ../../refseq/GCF*_2.0_assembly_report.txt # MT assembled-molecule MT Mitochondrion na <> NC_020006.2 non-nuclear 16516 na # 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 NC_020006.2 # this is actually ucscToRefSeq since this is a RefSeq assembly sort -k2 ucscToINSDC.txt > ucscToRefSeq.txt rm -f ucscToINSDC.txt awk '{printf "%s\t%s\n", $2, $1}' ucscToRefSeq.txt \ | sort > refSeqToUcsc.txt # chrM processing needs special help, fixup with the sed # extract the refseq vs. genbank names from the assembly_report # columns 5 and 7 are the INSDC and RefSeq names grep -v "^#" ../../refseq/GCF*_assembly_report.txt | cut -f5,7 \ | awk '{printf "%s\t%s\n", $2, $1}' | sed -e 's/na/JX946196.2/' \ | sort > refseq.insdc.txt awk '{printf "%s\t0\t%d\n", $1,$2}' ../../chrom.sizes \ | sort > ucsc.coordinate.tab join -2 2 refseq.insdc.txt ucscToRefSeq.txt | tr '[ ]' '[\t]' | sort -k3 \ | join -2 3 ucsc.coordinate.tab - | tr '[ ]' '[\t]' | cut -f1-4 \ > ucscToRefSeq.bed join -2 2 refseq.insdc.txt ucscToRefSeq.txt | tr '[ ]' '[\t]' | sort -k3 \ | join -2 3 ucsc.coordinate.tab - | tr '[ ]' '[\t]' | cut -f1-3,5 \ > ucscToINSDC.bed # verify chrM is correct: grep chrM *.bed # ucscToINSDC.bed:chrM 0 16516 JX946196.2 # ucscToRefSeq.bed:chrM 0 16516 NC_020006.2 # 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 * # 63251 refSeqToUcsc.txt # 63251 refseq.insdc.txt # 63251 ucsc.coordinate.tab # 63251 ucscToINSDC.bed # 63251 ucscToRefSeq.bed # 63251 ucscToRefSeq.txt 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 papAnu3 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 papAnu3 ucscToRefSeq ./ucscToRefSeq.sql ucscToRefSeq.bed # checkTableCoords should be silent checkTableCoords papAnu3 # each should cover %100 entirely: featureBits -countGaps papAnu3 ucscToINSDC # 2948397226 bases of 2948397226 (100.000%) in intersection featureBits -countGaps papAnu3 ucscToRefSeq # 2948397226 bases of 2948397226 (100.000%) in intersection ######################################################################### # add chromAlias table (DONE - 2017-06-20 - Hiram) mkdir /hive/data/genomes/papAnu3/bed/chromAlias cd /hive/data/genomes/papAnu3/bed/chromAlias hgsql -N -e 'select chrom,name from ucscToRefSeq;' papAnu3 \ | sort -k1,1 > ucsc.refseq.tab hgsql -N -e 'select chrom,name from ucscToINSDC;' papAnu3 \ | sort -k1,1 > ucsc.genbank.tab awk '{printf "%s\t%s\n", $1,$2}' ../ensLift/ucscToEns.txt \ | sort -k1,1 > ucsc.ensembl.tab ~/kent/src/hg/utils/automation/chromAlias.pl hgLoadSqlTab papAnu3 chromAlias ~/kent/src/hg/lib/chromAlias.sql \ papAnu3.chromAlias.tab ######################################################################### # fixup search rule for assembly track/gold table (DONE - 2017-06-20 - Hiram) cd ~/kent/src/hg/makeDb/trackDb/xenTro/papAnu3 # preview prefixes and suffixes: hgsql -N -e "select frag from gold;" papAnu3 \ | sed -e 's/[0-9][0-9]*//;' | sort | uniq -c # 198931 AHZZ.1 # 1 NC_.2 # implies a rule: '[AN][CH][Z_][Z0-9]+(\.[0-9]+)?' # verify this rule will find them all and eliminate them all: hgsql -N -e "select frag from gold;" papAnu3 | wc -l # 198932 hgsql -N -e "select frag from gold;" papAnu3 \ | egrep -e '[AN][CH][Z_][Z0-9]+(\.[0-9]+)?' | wc -l # 198932 hgsql -N -e "select frag from gold;" papAnu3 \ | egrep -v -e '[AN][CH][Z_][Z0-9]+(\.[0-9]+)?' | wc -l # 0 # hence, add to trackDb/chicken/papAnu3/trackDb.ra searchTable gold shortCircuit 1 termRegex [AN][CH][Z_][Z0-9]+(\.[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 - 2017-06-20 - Hiram) mkdir /hive/data/genomes/papAnu3/bed/repeatMasker cd /hive/data/genomes/papAnu3/bed/repeatMasker time (doRepeatMasker.pl -buildDir=`pwd` \ -bigClusterHub=ku -dbHost=hgwdev -workhorse=hgwdev \ -smallClusterHub=ku papAnu3) > do.log 2>&1 & # real 752m10.908s cat faSize.rmsk.txt # 2948397226 bases (55130419 N's 2893266807 real 1378626320 upper # 1514640487 lower) in 63251 sequences in 1 files # Total size: mean 46614.2 sd 2497421.7 min 200 (chrUn_NW_003880573v1) # max 220367699 (chr1) median 1416 # %51.37 masked total, %52.35 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 papAnu3 rmsk # 1515828879 bases of 2948397226 (51.412%) in intersection # real 1m14.038s # 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;' papAnu3 \ | bedSingleCover.pl stdin | ave -col=4 stdin | grep "^total" # total 1515828879.000000 # real 0m39.569s ########################################################################## # running simple repeat (DONE - 2017-06-20 - Hiram) mkdir /hive/data/genomes/papAnu3/bed/simpleRepeat cd /hive/data/genomes/papAnu3/bed/simpleRepeat # using trf409 5 here guessing smaller genome (human == 6) time (doSimpleRepeat.pl -buildDir=`pwd` -bigClusterHub=ku \ -dbHost=hgwdev -workhorse=hgwdev -smallClusterHub=ku \ -trf409 5 papAnu3) > do.log 2>&1 & # real 36m31.858s cat fb.simpleRepeat # 163817450 bases of 2893270787 (5.662%) in intersection # adding this trfMask to the other masking cd /hive/data/genomes/papAnu3 # when using the Window Masker result: # twoBitMask bed/windowMasker/papAnu3.cleanWMSdust.2bit \ # -add bed/simpleRepeat/trfMask.bed papAnu3.2bit # you can safely ignore the warning about fields >= 13 # when using Rmsk results, add to rmsk after it is done: twoBitMask papAnu3.rmsk.2bit \ -add bed/simpleRepeat/trfMask.bed papAnu3.2bit # you can safely ignore the warning about fields >= 13 twoBitToFa papAnu3.2bit stdout | faSize stdin > faSize.papAnu3.2bit.txt cat faSize.papAnu3.2bit.txt # 2948397226 bases (55130419 N's 2893266807 real 1377167920 upper # 1516098887 lower) in 63251 sequences in 1 files # Total size: mean 46614.2 sd 2497421.7 min 200 (chrUn_NW_003880573v1) # max 220367699 (chr1) median 1416 # %51.42 masked total, %52.40 masked real # reset the symlink rm /gbdb/papAnu3/papAnu3.2bit ln -s `pwd`/papAnu3.2bit /gbdb/papAnu3/papAnu3.2bit ######################################################################### # CREATE MICROSAT TRACK (DONE - 2017-06-21 - Hiram) ssh hgwdev mkdir /cluster/data/papAnu3/bed/microsat cd /cluster/data/papAnu3/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 papAnu3 microsat microsat.bed # Read 28500 elements of size 4 from microsat.bed ########################################################################## ## WINDOWMASKER (DONE - 2017-06-21 - Hiram) mkdir /hive/data/genomes/papAnu3/bed/windowMasker cd /hive/data/genomes/papAnu3/bed/windowMasker time (doWindowMasker.pl -buildDir=`pwd` -workhorse=hgwdev \ -dbHost=hgwdev papAnu3) > do.log 2>&1 # real 237m57.966s # Masking statistics cat faSize.papAnu3.cleanWMSdust.txt # 2948397226 bases (55130419 N's 2893266807 real 1766616003 upper 1126650804 lower) in 63251 sequences in 1 files # Total size: mean 46614.2 sd 2497421.7 min 200 (chrUn_NW_003880573v1) max 220367699 (chr1) median 1416 # %38.21 masked total, %38.94 masked real cat fb.papAnu3.rmsk.windowmaskerSdust.txt # 897063458 bases of 2948397226 (30.425%) in intersection ########################################################################## # run up idKeys files for ncbiRefSeq (DONE - 2017-06-21 - Hiram) mkdir /hive/data/genomes/papAnu3/bed/idKeys cd /hive/data/genomes/papAnu3/bed/idKeys time (doIdKeys.pl -buildDir=`pwd` papAnu3) > do.log 2>&1 & # real 70m22.608s cat papAnu3.keySignature.txt # 23214ba62fc59aeee20827fb5be54544 ########################################################################## # cpgIslands - (DONE - 2017-06-21 - Hiram) mkdir /hive/data/genomes/papAnu3/bed/cpgIslands cd /hive/data/genomes/papAnu3/bed/cpgIslands time (doCpgIslands.pl -dbHost=hgwdev -bigClusterHub=ku \ -workhorse=hgwdev -smallClusterHub=ku papAnu3) > do.log 2>&1 & # real 17m26.948s cat fb.papAnu3.cpgIslandExt.txt # 21276357 bases of 2893270787 (0.735%) in intersection ############################################################################## # genscan - (DONE - 2017-06-21 - Hiram) mkdir /hive/data/genomes/papAnu3/bed/genscan cd /hive/data/genomes/papAnu3/bed/genscan time (doGenscan.pl -buildDir=`pwd` -workhorse=hgwdev -dbHost=hgwdev \ -bigClusterHub=ku papAnu3) > do.log 2>&1 & # real 197m24.943s cat fb.papAnu3.genscan.txt # 52318577 bases of 2893270787 (1.808%) in intersection cat fb.papAnu3.genscanSubopt.txt # 51120501 bases of 2893270787 (1.767%) in intersection ############################################################################# # augustus gene track (DONE - 2017-06-21 - Hiram) mkdir /hive/data/genomes/papAnu3/bed/augustus cd /hive/data/genomes/papAnu3/bed/augustus time (doAugustus.pl -buildDir=`pwd` -bigClusterHub=ku \ -species=human -dbHost=hgwdev -workhorse=hgwdev papAnu3) > do.log 2>&1 & # real 119m13.121s cat fb.papAnu3.augustusGene.txt # 47314970 bases of 2893270787 (1.635%) in intersection ############################################################################# # lastz/chain/net swap human/hg38 (DONE - 2017-06-21 - Hiram) # original alignment cd /hive/data/genomes/hg38/bed/lastzPapAnu3.2017-06-21 cat fb.hg38.chainPapAnu3Link.txt # 2632683317 bases of 3049335806 (86.336%) in intersection # and for the swap: mkdir /hive/data/genomes/papAnu3/bed/blastz.hg38.swap cd /hive/data/genomes/papAnu3/bed/blastz.hg38.swap time (doBlastzChainNet.pl -verbose=2 \ /hive/data/genomes/hg38/bed/lastzPapAnu3.2017-06-21/DEF \ -swap -chainMinScore=3000 -chainLinearGap=medium \ -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \ -syntenicNet) > swap.log 2>&1 # real 232m5.391s cat fb.papAnu3.chainHg38Link.txt # 2501550280 bases of 2893270787 (86.461%) in intersection time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` papAnu3 hg38) \ > rbest.log 2>&1 # real 446m1.402s ######################################################################### # lastz/chain/net swap mouse/mm10 (DONE - 2017-06-21 - Hiram) # alignment to mouse/mm10: cd /hive/data/genomes/mm10/bed/lastzPapAnu3.2017-06-21 cat fb.mm10.chainPapAnu3Link.txt # 910628118 bases of 2652783500 (34.327%) in intersection mkdir /hive/data/genomes/papAnu3/bed/blastz.mm10.swap cd /hive/data/genomes/papAnu3/bed/blastz.mm10.swap time (doBlastzChainNet.pl -verbose=2 \ /hive/data/genomes/mm10/bed/lastzPapAnu3.2017-06-21/DEF \ -swap -syntenicNet \ -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \ -chainMinScore=3000 -chainLinearGap=medium) > swap.log 2>&1 # real 66m35.501s cat fb.papAnu3.chainMm10Link.txt # 897929517 bases of 2893270787 (31.035%) in intersection time (doRecipBest.pl -workhorse=hgwdev papAnu3 mm10 \ -buildDir=`pwd` -workhorse=hgwdev) > rbest.log 2>&1 & # real 578m46.893s ############################################################################## # Create kluster run files (DONE - 2017-06-21 - Hiram) # numerator is papAnu3 gapless bases "real" as reported by: featureBits -noRandom -noHap papAnu3 gap # 42059064 bases of 2682285126 (1.568%) 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 \( 2682285126 / 2861349177 \) \* 1024 # ( 2682285126 / 2861349177 ) * 1024 = 959.917787 # ==> use -repMatch=1025 same as papAnu2 cd /hive/data/genomes/papAnu3 blat papAnu3.2bit \ /dev/null /dev/null -tileSize=11 -makeOoc=jkStuff/papAnu3.11.ooc \ -repMatch=1025 # Wrote 29129 overused 11-mers to jkStuff/papAnu3.11.ooc # papAnu2 at repMatch=1025 was: # Wrote 29128 overused 11-mers to jkStuff/papAnu2.11.ooc # check non-bridged gaps to see what the typical size is: hgsql -N \ -e 'select * from gap where bridge="no" order by size;' papAnu3 \ | sort -k7,7nr | ave -col=7 stdin # Q1 100.000000 # median 100.000000 # Q3 100.000000 # average 100.000000 # min 100.000000 # max 100.000000 # count 9250 # total 925000.000000 # standard deviation 0.000000 # all these gap sizes are 100 gapToLift -verbose=2 -minGap=100 papAnu3 jkStuff/papAnu3.nonBridged.lft \ -bedFile=jkStuff/papAnu3.nonBridged.bed ######################################################################### # LIFTOVER TO papAnu2 (DONE - 2017-06-23 - Hiram) ssh hgwdev mkdir /hive/data/genomes/papAnu3/bed/blat.papAnu2.2017-06-23 cd /hive/data/genomes/papAnu3/bed/blat.papAnu2.2017-06-23 time (doSameSpeciesLiftOver.pl -verbose=2 -buildDir=`pwd` \ -ooc=/hive/data/genomes/papAnu3/jkStuff/papAnu3.11.ooc \ -bigClusterHub=ku -dbHost=hgwdev -workhorse=hgwdev \ papAnu3 papAnu2) > do.log 2>&1 # real 396m5.063s # verify the convert link on the test browser is now active from papAnu3 to # papAnu2 ######################################################################### # LIFTOVER TO papAnu4 (DONE - 2018-01-08 - Hiram) ssh hgwdev mkdir /hive/data/genomes/papAnu3/bed/blat.papAnu4.2018-01-08 cd /hive/data/genomes/papAnu3/bed/blat.papAnu4.2018-01-08 time (doSameSpeciesLiftOver.pl -verbose=2 -buildDir=`pwd` \ -ooc=/hive/data/genomes/papAnu3/jkStuff/papAnu3.11.ooc \ -bigClusterHub=ku -dbHost=hgwdev -workhorse=hgwdev \ papAnu3 papAnu4) > do.log 2>&1 & # real 579m54.169s # verify the convert link on the test browser is now active from papAnu3 to # papAnu3 ######################################################################### # GENBANK AUTO UPDATE (DONE - 2017-06-21 - Hiram) ssh hgwdev cd $HOME/kent/src/hg/makeDb/genbank git pull # /cluster/data/genbank/data/organism.lst shows: # #organism mrnaCnt estCnt refSeqCnt # Papio anubis 512 145626 505 # Papio anubis anubis 6 0 0 # Papio cynocephalus 23 0 0 # Papio cynocephalus x Papio anubis 3 0 0 # Papio hamadryas 102 0 0 # Papio hamadryas hamadryas 1 0 0 # Papio papio 10 0 0 # edit etc/genbank.conf to add papAnu3 just before papAnu2 # Baboon # papAnu3 (baboon) papAnu3.serverGenome = /hive/data/genomes/papAnu3/papAnu3.2bit papAnu3.clusterGenome = /hive/data/genomes/papAnu3/papAnu3.2bit papAnu3.ooc = /hive/data/genomes/papAnu3/jkStuff/papAnu3.11.ooc papAnu3.lift = /hive/data/genomes/papAnu3/jkStuff/papAnu3.nonBridged.lift papAnu3.perChromTables = no papAnu3.refseq.mrna.native.pslCDnaFilter = ${ordered.refseq.mrna.native.pslCDnaFilter} papAnu3.refseq.mrna.xeno.pslCDnaFilter = ${ordered.refseq.mrna.xeno.pslCDnaFilter} papAnu3.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter} papAnu3.genbank.mrna.xeno.pslCDnaFilter = ${ordered.genbank.mrna.xeno.pslCDnaFilter} papAnu3.genbank.est.native.pslCDnaFilter = ${ordered.genbank.est.native.pslCDnaFilter} papAnu3.genbank.est.xeno.pslCDnaFilter = ${ordered.genbank.est.xeno.pslCDnaFilter} papAnu3.downloadDir = papAnu3 # DO NOT NEED genbank.mrna.xeno except for human, mouse # defaults yes: genbank.mrna.native.load, genbank.mrna.native.loadDesc, # genbank.est.native.load, refseq.mrna.native.load, refseq.mrna.native.loadDesc, # refseq.mrna.xeno.load , refseq.mrna.xeno.loadDesc git commit -m 'adding papAnu3 baboon refs #19660' etc/genbank.conf git push # update /cluster/data/genbank/: make etc-update cd /cluster/data/genbank time ./bin/gbAlignStep -initial papAnu3 # logFile: var/build/logs/2017.06.21-10:02:02.papAnu3.initalign.log # real 422m26.969s tail -2 var/build/logs/2017.06.21-10:02:02.papAnu3.initalign.log # hgwdev 2017.06.21-17:01:26 papAnu3.initalign: Succeeded: papAnu3 # hgwdev 2017.06.21-17:04:29 papAnu3.initalign: finish # To re-do, rm the dir first: # /cluster/data/genbank/work/initial.papAnu3 # load database when finished ssh hgwdev cd /cluster/data/genbank time ./bin/gbDbLoadStep -drop -initialLoad papAnu3 # logFile: var/dbload/hgwdev/logs/2017.06.21-18:22:49.papAnu3.dbload.log # real 18m30.415s tail -1 var/dbload/hgwdev/logs/2017.06.21-18:22:49.papAnu3.dbload.log # hgwdev 2017.06.21-18:41:19 papAnu3.dbload: finish # enable daily alignment and update of hgwdev cd ~/kent/src/hg/makeDb/genbank git pull # add papAnu3 to: # etc/align.dbs etc/hgwdev.dbs git add etc/align.dbs etc/hgwdev.dbs git commit -m 'adding papAnu3 to the update alignments refs #19660' etc/align.dbs etc/hgwdev.dbs git push make etc-update ############################################################################# # ncbiRefSeq (TBD - 2016-05-13 - Hiram) mkdir /hive/data/genomes/papAnu3/bed/ncbiRefSeq cd /hive/data/genomes/papAnu3/bed/ncbiRefSeq # running step wise as this script is still under development time (~/kent/src/hg/utils/automation/doNcbiRefSeq.pl -buildDir=`pwd` \ -bigClusterHub=ku -dbHost=hgwdev \ -stop=download -fileServer=hgwdev -smallClusterHub=ku -workhorse=hgwdev \ refseq vertebrate_other Gallus_gallus \ GCF_000002315.4_Gallus_gallus-5.0 papAnu3) > download.log 2>&1 # real 16m29.536s time (~/kent/src/hg/utils/automation/doNcbiRefSeq.pl -buildDir=`pwd` \ -continue=process -bigClusterHub=ku -dbHost=hgwdev \ -stop=process -fileServer=hgwdev -smallClusterHub=ku -workhorse=hgwdev \ refseq vertebrate_other Gallus_gallus \ GCF_000002315.4_Gallus_gallus-5.0 papAnu3) > process.log 2>&1 # real 3m58.858s time (~/kent/src/hg/utils/automation/doNcbiRefSeq.pl -buildDir=`pwd` \ -continue=load -bigClusterHub=ku -dbHost=hgwdev \ -stop=load -fileServer=hgwdev -smallClusterHub=ku -workhorse=hgwdev \ refseq vertebrate_other Gallus_gallus \ GCF_000002315.4_Gallus_gallus-5.0 papAnu3) > load.log 2>&1 # real 0m33.205s cat fb.ncbiRefSeq.papAnu3.txt # 82563006 bases of 1218501075 (6.776%) in intersection featureBits -enrichment papAnu3 refGene ncbiRefSeq # refGene 1.181%, ncbiRefSeq 6.776%, both 1.175%, cover 99.49%, # enrich 14.68x ######################################################################### # BLATSERVERS ENTRY (DONE - 2017-06-23 - 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 ("papAnu3", "blat1c", "17892", "1", "0"); \ INSERT INTO blatServers (db, host, port, isTrans, canPcr) \ VALUES ("papAnu3", "blat1c", "17893", "0", "1");' \ hgcentraltest # test it with some sequence ############################################################################ ## reset default position to same as what hg38 has ## (DONE - 2017-06-23 - Hiram) ssh hgwdev hgsql -e 'update dbDb set defaultPos="chr1:13964116-14118692" where name="papAnu3";' hgcentraltest ######################################################################### # all.joiner update, downloads and in pushQ - (DONE - 2017-06-23 - Hiram) cd $HOME/kent/src/hg/makeDb/schema # fixup all.joiner until this is a clean output joinerCheck -database=papAnu3 -tableCoverage all.joiner joinerCheck -database=papAnu3 -times all.joiner joinerCheck -database=papAnu3 -keys all.joiner cd /hive/data/genomes/papAnu3 time (makeDownloads.pl -workhorse=hgwdev papAnu3) > downloads.log 2>&1 # real 26m28.250s # now ready for pushQ entry mkdir /hive/data/genomes/papAnu3/pushQ cd /hive/data/genomes/papAnu3/pushQ time (makePushQSql.pl -redmineList papAnu3) > papAnu3.pushQ.sql 2> stderr.out # real 3m42.117s # check for errors in stderr.out, some are OK, e.g.: # WARNING: papAnu3 does not have seq # WARNING: papAnu3 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/papAnu3/pushQ/redmine.papAnu3.file.list /hive/data/genomes/papAnu3/pushQ/redmine.papAnu3.releaseLog.txt /hive/data/genomes/papAnu3/pushQ/redmine.papAnu3.table.list #########################################################################