# for emacs: -*- mode: sh; -*- # This file describes browser build for the hpv1 ######################################################################### # micrograph photograph from cancer.gov # (DONE - 2017-05-10 - Hiram) mkdir -p /hive/data/genomes/hpv1/photo cd /hive/data/genomes/hpv1/photo wget -O cancer.gov.jpg \ "https://visualsonline.cancer.gov/retrieve.cfm?imageid=2255&dpi=300&fileformat=jpg" convert -quality 80 -geometry 350x350 cancer.gov.jpg hpv1.jpg printf 'photoCreditURL\thttps://commons.wikimedia.org/wiki/File:Papilloma_virus_(hpv).jpg photoCreditName\tNIH National Cancer Institute ' > photoReference.txt cat photoReference.txt photoCreditURL https://commons.wikimedia.org/wiki/File:Papilloma_virus_(hpv).jpg photoCreditName NIH National Cancer Institute # Checking in that photograph to the source tree, will need to fixup the # description.html page to correctly reference this photo since # our scripts use the scientific name to find the photo ######################################################################### # Initial steps (DONE - 2017-05-10 - Hiram) # This initialBuild.txt document was started from criGriChoV1 # version of initialBuild.txt mkdir /hive/data/genomes/hpv1/refseq cd /hive/data/genomes/hpv1/refseq export accession="GCF_000862685.1" export asmId="ViralProj15424" export level0="GCF" export level1="000" export level2="862" export level3="685" rsync -L -a -P rsync://ftp.ncbi.nlm.nih.gov/genomes/all/$level0/$level1/$level2/$level3/${accession}_${asmId}/ ./ # sent 279 bytes received 50441 bytes 20288.00 bytes/sec # total size is 48785 speedup is 0.96 # real 0m1.239s # check assembly size for later reference: faSize G*424_genomic.fna.gz # 8033 bases (0 N's 8033 real 8033 upper 0 lower) in 1 sequences in 1 files # this information is from the top of # hpv1/refseq/GCF_000862685.1_ViralProj15424_assembly_report.txt # Assembly name: ViralProj15424 # Organism name: Human papillomavirus type 90 (viruses) # Taxid: 333769 # BioProject: PRJNA15424 # Submitter: Albert Einstein College of Medicine, Microbiology & Immunology, USA, Bronx, New York # Date: 2002-8-5 # Assembly type: n/a # Release type: major # Assembly level: Complete Genome # Genome representation: full # RefSeq assembly accession: GCF_000862685.1 # ## Assembly-Units: ## GenBank Unit Accession RefSeq Unit Accession Assembly-Unit name ## GCF_000862675.1 Primary assembly ############################################################################# # establish config.ra file (DONE - Hiram - 2017-05-10) # arguments here are: cd /hive/data/genomes/hpv1 $HOME/kent/src/hg/utils/automation/prepConfig.pl hpv1 virus \ HPV ./refseq/*_assembly_report.txt > hpv1.config.ra # going to need a mitoAcc ? # unfortunately, there is no bioSample, set to n/a # will need to fixup resulting description.html # set: mitoAcc none # set: commonName HPV # set: orderKey 8700 (common name alphabetic) # to see order keys to verify this one is correct: # hgsql -e 'select name,organism,orderKey from dbDb order by orderKey;' \ # hgcentraltest | less # verify it looks sane cat hpv1.config.ra # config parameters for makeGenomeDb.pl: db hpv1 clade virus genomeCladePriority 2000 scientificName Human papillomavirus type 90 commonName HPV assemblyDate Aug. 2002 assemblyLabel Albert Einstein College of Medicine, Microbiology & Immunology, USA, Bronx, New York assemblyShortLabel ViralProj15424 orderKey 8700 mitoAcc none fastaFiles /hive/data/genomes/hpv1/ucsc/*.fa.gz agpFiles /hive/data/genomes/hpv1/ucsc/*.agp # qualFiles none dbDbSpeciesDir HPV photoCreditURL https://commons.wikimedia.org/wiki/File:Papilloma_virus_(hpv).jpg photoCreditName NIH National Cancer Institute ncbiGenomeId 5533 ncbiAssemblyId 265281 ncbiAssemblyName ViralProj15424 ncbiBioProject 15424 ncbiBioSample n/a genBankAccessionID GCF_000862685.1 taxId 333769 ############################################################################# # setup UCSC named files (DONE - 2017-05-10 - Hiram) mkdir /hive/data/genomes/hpv1/ucsc cd /hive/data/genomes/hpv1/ucsc # one simple sequence: zcat ../refseq/GCF_000862685.1_ViralProj15424_genomic.fna.gz \ | sed -e 's/^>NC_004104.1.*/>NC_004104v1/;' | gzip > chr.fa.gz printf "NC_004104v1\t1\t8033\t1\tF\tNC_004104.1\t1\t8033\t+\n" > chr.agp # verify OK: checkAgpAndFa chr.agp chr.fa.gz # Valid Fasta file entry # All AGP and FASTA entries agree - both files are valid ############################################################################# # Initial database build (DONE - 2017-05-10 - Hiram) cd /hive/data/genomes/hpv1 # verify sequence and AGP are OK: time (makeGenomeDb.pl -workhorse=hgwdev -dbHost=hgwdev -fileServer=hgwdev \ -stop=agp hpv1.config.ra) > agp.log 2>&1 # real 0m9.024s # then finish it off: (will break down in trackDb step due to # photograph name. Attempt to avoid this # in /usr/local/apache/htdocs/images # ln -s hpv1.jpg 'Human_papillomavirus_type_90'.jpg time (makeGenomeDb.pl -workhorse=hgwdev -dbHost=hgwdev \ -fileServer=hgwdev -continue=db hpv1.config.ra) > db.log 2>&1 # real 0m10.396s time (makeGenomeDb.pl -workhorse=hgwdev -dbHost=hgwdev \ -continue=trackDb -fileServer=hgwdev -continue=db hpv1.config.ra) > trackDb.log 2>&1 # remove the temporary symlink, edit the description.html page # check in the trackDb files created in TemporaryTrackDbCheckout/ # and add hpv1 to trackDb/makefile # temporary symlink until masked sequence is available cd /hive/data/genomes/hpv1 ln -s `pwd`/hpv1.unmasked.2bit /gbdb/hpv1/hpv1.2bit ############################################################################## # cpgIslands on UNMASKED sequence (DONE - 2017-05-10 - Hiram) mkdir /hive/data/genomes/hpv1/bed/cpgIslandsUnmasked cd /hive/data/genomes/hpv1/bed/cpgIslandsUnmasked time (doCpgIslands.pl -dbHost=hgwdev -bigClusterHub=ku -buildDir=`pwd` \ -tableName=cpgIslandExtUnmasked \ -maskedSeq=/hive/data/genomes/hpv1/hpv1.unmasked.2bit \ -workhorse=hgwdev -smallClusterHub=ku hpv1) > do.log 2>&1 # real 0m37.362s cat fb.hpv1.cpgIslandExtUnmasked.txt # 203 bases of 8033 (2.527%) in intersection ############################################################################# # cytoBandIdeo - (DONE - 2017-05-10 - Hiram) mkdir /hive/data/genomes/hpv1/bed/cytoBand cd /hive/data/genomes/hpv1/bed/cytoBand makeCytoBandIdeo.csh hpv1 ######################################################################### # ucscToINSDC and ucscToRefSeq table/track (DONE - 2017-05-10 - Hiram) # really simple situation here, only one name to deal with mkdir /hive/data/genomes/hpv1/bed/ucscToINSDC cd /hive/data/genomes/hpv1/bed/ucscToINSDC # lookup the INSDC name at: # https://www.ncbi.nlm.nih.gov/genome/?term=txid931244[orgn] printf "NC_004104v1\t0\t8033\tNC_004104.1\n" > ucscToRefSeq.bed printf "NC_004104v1\t0\t8033\tAY057438.1\n" > ucscToINSDC.bed export chrSize=`cut -f1 ucscToINSDC.bed | awk '{print length($0)}' | sort -n | tail -1` echo $chrSize # 11 # use the chrSize in this sed sed -e "s/21/$chrSize/" $HOME/kent/src/hg/lib/ucscToINSDC.sql \ | hgLoadSqlTab hpv1 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 $chrSize # 11 sed -e "s/21/$chrSize/" $HOME/kent/src/hg/lib/ucscToINSDC.sql \ | sed -e 's/INSDC/RefSeq/g;' > ucscToRefSeq.sql hgLoadSqlTab hpv1 ucscToRefSeq ./ucscToRefSeq.sql ucscToRefSeq.bed # checkTableCoords should be silent checkTableCoords hpv1 # each should cover %100 entirely: featureBits -countGaps hpv1 ucscToINSDC # 8033 bases of 8033 (100.000%) in intersection featureBits -countGaps hpv1 ucscToRefSeq # 8033 bases of 8033 (100.000%) in intersection ######################################################################### # add chromAlias table (DONE - 2017-05-10 - Hiram) mkdir /hive/data/genomes/hpv1/bed/chromAlias cd /hive/data/genomes/hpv1/bed/chromAlias hgsql -N -e 'select chrom,name,"refseq" from ucscToRefSeq;' hpv1 \ > ucsc.refseq.tab hgsql -N -e 'select chrom,name,"genbank" from ucscToINSDC;' hpv1 \ > ucsc.genbank.tab awk '{printf "%s\t%s\t%s\n", $2,$1,$3}' ucsc.genbank.tab ucsc.refseq.tab \ | sort > hpv1.chromAlias.tab cat hpv1.chromAlias.tab # AY057438.1 NC_004104v1 genbank # NC_004104.1 NC_004104v1 refseq hgLoadSqlTab hpv1 chromAlias ~/kent/src/hg/lib/chromAlias.sql \ hpv1.chromAlias.tab ######################################################################### # fixup search rule for assembly track/gold table (DONE - 2017-05-10 - Hiram) cd ~/kent/src/hg/makeDb/trackDb/criGri/hpv1 # preview prefixes and suffixes: hgsql -N -e "select frag from gold;" hpv1 \ | sed -e 's/[0-9][0-9]*//;' | sort | uniq -c # 1 NC_.1 # implies a rule: 'NC_[0-9]+(\.[0-9]+)?' # verify this rule will find them all and eliminate them all: hgsql -N -e "select frag from gold;" hpv1 | wc -l # 1 hgsql -N -e "select frag from gold;" hpv1 \ | egrep -e 'NC_[0-9]+(\.[0-9]+)?' | wc -l # 1 hgsql -N -e "select frag from gold;" hpv1 \ | egrep -v -e 'NC_[0-9]+(\.[0-9]+)?' | wc -l # 0 # hence, add to trackDb/chicken/hpv1/trackDb.ra searchTable gold shortCircuit 1 termRegex NC_[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 - 2017-05-10 - Hiram) # RepeatMasker doesn't know about this virus sequence name as is, # scientificName Human papillomavirus type 90 # and there is nothing related in the taxonomy.dat table in RM. # However, there is a generic 'viruses' name, taxId 10239 mkdir /hive/data/genomes/hpv1/bed/repeatMasker cd /hive/data/genomes/hpv1/bed/repeatMasker time (doRepeatMasker.pl -buildDir=`pwd` \ -species "viruses" -bigClusterHub=ku -dbHost=hgwdev -workhorse=hgwdev \ -smallClusterHub=ku hpv1) > do.log 2>&1 & # real 3m6.878s # looks like it ends up with one single repeat: # 16 26.7 3.6 1.8 NC_004104v1 7405 7480 (553) + (TG)n Simple_repeat 1 77 (0) 1 # and it fails with an empty nestedRepeats file during load # help the doLoad step finish: ln -s `pwd`/hpv1.rmsk.2bit /hive/data/genomes/hpv1/hpv1.rmsk.2bit # continue with cleanUp: time (doRepeatMasker.pl -buildDir=`pwd` \ -species "viruses" -bigClusterHub=ku -dbHost=hgwdev -workhorse=hgwdev \ -continue=cleanup -smallClusterHub=ku hpv1) > cleanup.log 2>&1 & # real 0m4.568s cat faSize.rmsk.txt # 8033 bases (0 N's 8033 real 7957 upper 76 lower) in 1 sequences in 1 files # %0.95 masked total, %0.95 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 hpv1 rmsk # 76 bases of 8033 (0.946%) in intersection # real 0m0.024s # why is it different than the faSize above ? (It isn't there are no gaps) # 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;' hpv1 \ | bedSingleCover.pl stdin | ave -col=4 stdin | grep "^total" # total 76.000000 # real 0m0.029s ########################################################################## # running simple repeat (DONE - 2017-05-10 - Hiram) mkdir /hive/data/genomes/hpv1/bed/simpleRepeat cd /hive/data/genomes/hpv1/bed/simpleRepeat # using trf409 1 here (human == 6) time (doSimpleRepeat.pl -buildDir=`pwd` -bigClusterHub=ku \ -dbHost=hgwdev -workhorse=hgwdev -smallClusterHub=ku \ -trf409 1 hpv1) > do.log 2>&1 & # XXX - there are no simple repeats, empty result # real 0m13.037s ######################################################################### # CREATE MICROSAT TRACK (TBD - 2017-04-11 - Hiram) # XXX - there are no simple repeats ssh hgwdev mkdir /cluster/data/hpv1/bed/microsat cd /cluster/data/hpv1/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 hpv1 microsat microsat.bed # Read 213828 elements of size 4 from microsat.bed ########################################################################## ## WINDOWMASKER (DONE - 2017-04-11 - Hiram) mkdir /hive/data/genomes/hpv1/bed/windowMasker cd /hive/data/genomes/hpv1/bed/windowMasker time (doWindowMasker.pl -buildDir=`pwd` -workhorse=hgwdev \ -dbHost=hgwdev hpv1) > do.log 2>&1 # real 299m17.427s # finished before RepeatMasker, failed on featureBits rmsk, so finish # this off time (doWindowMasker.pl -buildDir=`pwd` -workhorse=hgwdev \ -continue=cleanup -dbHost=hgwdev hpv1) > cleanup.log 2>&1 # Masking statistics cat faSize.hpv1.cleanWMSdust.txt # 8033 bases (0 N's 8033 real 7715 upper 318 lower) in 1 sequences in 1 files # %3.96 masked total, %3.96 masked real cat fb.hpv1.rmsk.windowmaskerSdust.txt # 76 bases of 8033 (0.946%) in intersection # check to see what the addition together would be # for rmsk and WM: featureBits -or -countGaps hpv1 rmsk windowmaskerSdust \ > fb.hpv1.rmsk+windowmaskerSdust.txt 2>&1 cat fb.hpv1.rmsk+windowmaskerSdust.txt # 318 bases of 8033 (3.959%) in intersection # using the Window Masker result by itself: cd /hive/data/genomes/hpv1 twoBitMask hpv1.unmasked.2bit \ -type=.bed -add bed/windowMasker/cleanWMask.bed.gz hpv1.2bit # you can safely ignore the warning about fields >= 13 twoBitToFa hpv1.2bit stdout \ | faSize stdin > faSize.hpv1.2bit.txt cat faSize.hpv1.2bit.txt # 8033 bases (0 N's 8033 real 7715 upper 318 lower) in 1 sequences in 1 files # %3.96 masked total, %3.96 masked real # reset the symlink rm /gbdb/hpv1/hpv1.2bit ln -s `pwd`/hpv1.2bit /gbdb/hpv1/hpv1.2bit ########################################################################## # run up idKeys files for ncbiRefSeq (DONE - 2017-05-10 - Hiram) mkdir /hive/data/genomes/hpv1/bed/idKeys cd /hive/data/genomes/hpv1/bed/idKeys time (doIdKeys.pl -buildDir=`pwd` hpv1) > do.log 2>&1 & # real 0m17.364s cat hpv1.keySignature.txt # a1821a8fb20b88bd25f0eacea585b24a ########################################################################## # cpgIslands - (DONE - 2017-05-10 - Hiram) mkdir /hive/data/genomes/hpv1/bed/cpgIslands cd /hive/data/genomes/hpv1/bed/cpgIslands time (doCpgIslands.pl -dbHost=hgwdev -bigClusterHub=ku \ -workhorse=hgwdev -smallClusterHub=ku hpv1) > do.log 2>&1 & # real 0m36.957s cat fb.hpv1.cpgIslandExt.txt # 203 bases of 8033 (2.527%) in intersection ############################################################################## # genscan - (DONE - 2017-05-10 - Hiram) mkdir /hive/data/genomes/hpv1/bed/genscan cd /hive/data/genomes/hpv1/bed/genscan time (doGenscan.pl -buildDir=`pwd` -workhorse=hgwdev -dbHost=hgwdev \ -bigClusterHub=ku hpv1) > do.log 2>&1 & # real 0m52.467s cat fb.hpv1.genscan.txt # 3408 bases of 8033 (42.425%) in intersection cat fb.hpv1.genscanSubopt.txt # 3144 bases of 8033 (39.139%) in intersection ############################################################################# # augustus gene track (TBD - 2017-04-13 - Hiram) # XXX augustus can not do virus sequence mkdir /hive/data/genomes/hpv1/bed/augustus cd /hive/data/genomes/hpv1/bed/augustus time (doAugustus.pl -buildDir=`pwd` -bigClusterHub=ku \ -species=human -dbHost=hgwdev -workhorse=hgwdev hpv1) > do.log 2>&1 & # real 72m23.671s cat fb.hpv1.augustusGene.txt # 29811614 bases of 2318132242 (1.286%) in intersection ############################################################################## # Create kluster run files (TBD - 2017-04-13 - Hiram) # numerator is hpv1 gapless bases "real" as reported by: featureBits -noRandom -noHap hpv1 gap # 0 bases of 8033 (0.000%) 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 \( 8033 / 2861349177 \) \* 1024 # ( 8033 / 2861349177 ) * 1024 = 0.002875 # repMatch=1 produces 1,459 overused 11-mers $ repMatch=2 produces 1 overused 11-mers $ repMatch=3 produces 0 overused 11-mers # ==> use -repMatch=3, do not need to mask anything cd /hive/data/genomes/hpv1 blat hpv1.2bit \ /dev/null /dev/null -tileSize=11 -makeOoc=jkStuff/hpv1.11.ooc \ -repMatch=3 # Wrote 0 overused 11-mers to jkStuff/hpv1.11.ooc # check non-bridged gaps to see what the typical size is: # there are no non-bridged gaps in this assembly: hgsql -N -e 'select bridge from gap;' hpv1 | sort | uniq -c # no output, nothing to see here ######################################################################### # GENBANK AUTO UPDATE (TBD - 2017-04-13 - Hiram) ssh hgwdev cd $HOME/kent/src/hg/makeDb/genbank git pull # /cluster/data/genbank/data/organism.lst shows: # organism mrnaCnt estCnt refSeqCnt # Human papillomavirus 61 0 0 # Human papillomavirus type 16 21 2 0 # Human papillomavirus type 18 9 0 0 # Human papillomavirus type 197 1 0 0 # Human papillomavirus type 38 1 0 0 # Human papillomavirus type 45 1 0 0 # Human papillomavirus type 58 2 0 0 # Human papillomavirus type 68 2 0 0 # Human papillomavirus type 6b 1 0 0 # edit etc/genbank.conf to add hpv1 at the end # hpv1 (Human papillomavirus type 90 - Taxid: 333769) hpv1.serverGenome = /hive/data/genomes/hpv1/hpv1.2bit hpv1.clusterGenome = /hive/data/genomes/hpv1/hpv1.2bit hpv1.ooc = /hive/data/genomes/hpv1/jkStuff/hpv1.11.ooc hpv1.lift = no hpv1.downloadDir = hpv1 hpv1.perChromTables = no hpv1.refseq.mrna.native.pslCDnaFilter = ${finished.refseq.mrna.native.pslCDnaFilter} hpv1.refseq.mrna.xeno.pslCDnaFilter = ${finished.refseq.mrna.xeno.pslCDnaFilter} hpv1.genbank.mrna.native.pslCDnaFilter = ${finished.genbank.mrna.native.pslCDnaFilter} hpv1.genbank.mrna.xeno.pslCDnaFilter = ${finished.genbank.mrna.xeno.pslCDnaFilter} hpv1.genbank.est.native.pslCDnaFilter = ${finished.genbank.est.native.pslCDnaFilter} # 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 # hpv1.upstreamGeneTbl = ensGene # hpv1.upstreamMaf = multiz9way /hive/data/genomes/hpv1/bed/multiz9way/species.list git commit -m 'adding hpv1 Human papillomavirus type 90 - refs #18971' etc/genbank.conf src/lib/gbGenome.c git push # update /cluster/data/genbank/: make etc-update make install-server cd /cluster/data/genbank time ./bin/gbAlignStep -initial hpv1 # logFile: var/build/logs/2017.05.10-18:36:54.hpv1.initalign.log # real 1354m21.533s tail -2 var/build/logs/2017.05.10-18:36:54.hpv1.initalign.log # hgwdev 2017.05.11-17:11:12 hpv1.initalign: Succeeded: hpv1 # hgwdev 2017.05.11-17:11:15 hpv1.initalign: finish # To re-do, rm the dir first: # /cluster/data/genbank/work/initial.hpv1 # load database when finished ssh hgwdev cd /cluster/data/genbank time ./bin/gbDbLoadStep -drop -initialLoad hpv1 # logFile: var/dbload/hgwdev/logs/2017.05.11-23:06:35.hpv1.dbload.log # about 90 minutes, appears to load nothing ? tail -1 var/dbload/hgwdev/logs/2017.05.11-23:06:35.hpv1.dbload.log # hgwdev 2017.05.12-00:35:31 hpv1.dbload: finish XXX -checking with genbank master on zero results - Fri May 12 08:19:39 PDT 2017 # enable daily alignment and update of hgwdev cd ~/kent/src/hg/makeDb/genbank git pull # add hpv1 to: # etc/align.dbs etc/hgwdev.dbs git add etc/align.dbs etc/hgwdev.dbs git commit -m 'adding hpv1 to the update alignments refs #19228' etc/align.dbs etc/hgwdev.dbs git push make etc-update ############################################################################# # ncbiGene (DONE - 2017-05-10 - Hiram) mkdir /hive/data/genomes/hpv1/bed/ncbiGene cd /hive/data/genomes/hpv1/bed/ncbiGene # switching the names from column 1 to 12 and 12 to 1 with the awk: gff3ToGenePred -useName -attrsOut=hpv1.attrs.tab -geneNameAttr=gene \ ../../refseq/GCF_000862685.1_ViralProj15424_genomic.gff.gz \ stdout | sed -e 's/NC_004104.1/NC_004104v1/;' \ | awk -F'\t' '{print $12,$2,$3,$4,$5,$6,$7,$8,$9,$10,$11,$1,$13,$14,$15}' | tr '[ ]' '[\t]' > hpv1.ncbiGene.gp # NP_671509.1 NC_004104v1 + 5791 7309 5791 7309 1 5791, 7309, 0 L1 cmpl cmpl 0, # becomes: # L1 NC_004104v1 + 5791 7309 5791 7309 1 5791, 7309, 0 NP_671509.1 cmpl cmpl 0, genePredCheck -db=hpv1 hpv1.ncbiGene.gp # checked: 7 failed: 0 hgLoadGenePred -genePredExt hpv1 ncbiGene hpv1.ncbiGene.gp genePredCheck -db=hpv1 ncbiGene # checked: 7 failed: 0 XXX - more name wrangling is in order XXX - need to get gene descriptions out of the genbank record ######################################################################### # BLATSERVERS ENTRY (TBD - 2017-04-19 - 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 ("hpv1", "blat1a", "17872", "1", "0"); \ INSERT INTO blatServers (db, host, port, isTrans, canPcr) \ VALUES ("hpv1", "blat1a", "17873", "0", "1");' \ hgcentraltest # test it with some sequence ############################################################################ ## set default position to SRC gene sequence from human protein blat ## (TBD - 2017-04-19 - Hiram) ssh hgwdev hgsql -e 'update dbDb set defaultPos="NW_003613641v1:1277445-1295702" where name="hpv1";' hgcentraltest ######################################################################### # all.joiner update, downloads and in pushQ - (TBD - 2017-04-25 - Hiram) cd $HOME/kent/src/hg/makeDb/schema # fixup all.joiner until this is a clean output joinerCheck -database=hpv1 -tableCoverage all.joiner joinerCheck -database=hpv1 -times all.joiner joinerCheck -database=hpv1 -keys all.joiner cd /hive/data/genomes/hpv1 time (makeDownloads.pl -workhorse=hgwdev hpv1) > downloads.log 2>&1 # real 22m35.669s # now ready for pushQ entry mkdir /hive/data/genomes/hpv1/pushQ cd /hive/data/genomes/hpv1/pushQ time (makePushQSql.pl -redmineList hpv1) \ > hpv1.pushQ.sql 2> stderr.out # real 7m21.629s # check for errors in stderr.out, some are OK, e.g.: # WARNING: hgwdev does not have /gbdb/hpv1/wib/gc5Base.wib # WARNING: hgwdev does not have /gbdb/hpv1/wib/quality.wib # WARNING: hgwdev does not have /gbdb/hpv1/bbi/quality.bw # WARNING: hpv1 does not have seq # WARNING: hpv1 does not have extFile # enter the path names to the redmine listings in the redmine issue # refs 19228 #########################################################################