# for emacs: -*- mode: sh; -*- # This file describes browser build for the hbv1 ######################################################################### # viron diagram found on WikiMedia Commons # (DONE - 2017-06-02 - Hiram) mkdir -p /hive/data/genomes/hbv1/photo cd /hive/data/genomes/hbv1/photo wget -O wikiMediaCommons.hbv.png \ https://upload.wikimedia.org/wikipedia/commons/7/78/HBV.png convert -quality 80 -geometry 350x350 wikiMediaCommons.hbv.png hbv1.jpg cd /hive/data/genomes/hbv1 printf 'photoCreditURL\thttps://commons.wikimedia.org/wiki/File:HBV.png photoCreditName\tWikiMedia Commons: Dr. Graham Beards ' > photoReference.txt cat photoReference.txt photoCreditURL https://commons.wikimedia.org/wiki/File:HBV.png photoCreditName WikiMedia Commons: Dr. Graham Beards # 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 - 2017-06-02 - Hiram) # This initialBuild.txt document was started from hpv1 # version of initialBuild.txt sed -e 's/pv1/bv1/g; s/DONE/TBD/g;' ../hpv1/initialBuild.txt > initialBuild.txt mkdir /hive/data/genomes/hbv1/refseq cd /hive/data/genomes/hbv1/refseq viral/Hepatitis_B_virus/all_assembly_versions/GCF_000861825.2_ViralProj15428 export accession="GCF_000861825.2" export asmId="ViralProj15428" export level0="GCF" export level1="000" export level2="861" export level3="825" time rsync -L -a -P rsync://ftp.ncbi.nlm.nih.gov/genomes/all/$level0/$level1/$level2/$level3/${accession}_${asmId}/ ./ # sent 298 bytes received 48050 bytes 32232.00 bytes/sec # total size is 46296 speedup is 0.96 # real 0m1.422s # check assembly size for later reference: faSize G*428_genomic.fna.gz # 3182 bases (0 N's 3182 real 3182 upper 0 lower) in 1 sequences in 1 files # this information is from the top of # hbv1/refseq/GCF_000861825.2_ViralProj15428_assembly_report.txt # Assembly name: ViralProj15428 # Organism name: Hepatitis B virus (viruses) # Taxid: 10407 # BioProject: PRJNA15428 # Submitter: NCBI Genome Project # Date: 1993-4-21 # Assembly type: n/a # Release type: major # Assembly level: Complete Genome # Genome representation: full # RefSeq assembly accession: GCF_000861825.2 # ## Assembly-Units: ## GenBank Unit Accession RefSeq Unit Accession Assembly-Unit name ## GCF_000861815.2 Primary assembly ############################################################################# # establish config.ra file (DONE - Hiram - 2017-06-02) # arguments here are: cd /hive/data/genomes/hbv1 $HOME/kent/src/hg/utils/automation/prepConfig.pl hbv1 virus \ HBV ./refseq/*_assembly_report.txt > hbv1.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 HBV # set: orderKey 8100 (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 hbv1.config.ra # config parameters for makeGenomeDb.pl: db hbv1 clade virus genomeCladePriority 2000 scientificName Hepatitis B virus commonName HBV assemblyDate Apr. 1993 assemblyLabel NCBI Genome Project assemblyShortLabel ViralProj15428 orderKey 8100 mitoAcc none fastaFiles /hive/data/genomes/hbv1/ucsc/*.fa.gz agpFiles /hive/data/genomes/hbv1/ucsc/*.agp # qualFiles none dbDbSpeciesDir HBV photoCreditURL https://commons.wikimedia.org/wiki/File:HBV.png photoCreditName WikiMedia Commons: Dr. Graham Beards ncbiGenomeId 5536 ncbiAssemblyId 559321 ncbiAssemblyName ViralProj15428 ncbiBioProject 15428 ncbiBioSample n/a genBankAccessionID GCF_000861825.2 taxId 10407 ############################################################################# # setup UCSC named files (DONE - 2017-06-02 - Hiram) mkdir /hive/data/genomes/hbv1/ucsc cd /hive/data/genomes/hbv1/ucsc # one simple sequence: zcat ../refseq/GCF_000861825.2_ViralProj15428_genomic.fna.gz \ | sed -e 's/^>NC_003977.2.*/>NC_003977v2/;' | gzip > chr.fa.gz printf "NC_003977v2\t1\t3182\t1\tF\tNC_003977.2\t1\t3182\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 (TBD - 2017-05-10 - Hiram) cd /hive/data/genomes/hbv1 # verify sequence and AGP are OK: time (makeGenomeDb.pl -workhorse=hgwdev -dbHost=hgwdev -fileServer=hgwdev \ -stop=agp hbv1.config.ra) > agp.log 2>&1 # real 0m8.535s # 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 hbv1.jpg Hepatitis_B_virus.jpg time (makeGenomeDb.pl -workhorse=hgwdev -dbHost=hgwdev \ -fileServer=hgwdev -continue=db hbv1.config.ra) > db.log 2>&1 # real 0m10.027s time (makeGenomeDb.pl -workhorse=hgwdev -dbHost=hgwdev \ -continue=trackDb -fileServer=hgwdev hbv1.config.ra) > trackDb.log 2>&1 # real 0m6.801s # remove the temporary symlink, edit the description.html page # fixup photo URL to hbv1.jpg and the BioSample n/a # check in the trackDb files created in TemporaryTrackDbCheckout/ # and add hbv1 to trackDb/makefile # temporary symlink until masked sequence is available cd /hive/data/genomes/hbv1 ln -s `pwd`/hbv1.unmasked.2bit /gbdb/hbv1/hbv1.2bit ############################################################################## # cpgIslands on UNMASKED sequence (DONE - 2017-06-02 - Hiram) mkdir /hive/data/genomes/hbv1/bed/cpgIslandsUnmasked cd /hive/data/genomes/hbv1/bed/cpgIslandsUnmasked time (doCpgIslands.pl -dbHost=hgwdev -bigClusterHub=ku -buildDir=`pwd` \ -tableName=cpgIslandExtUnmasked \ -maskedSeq=/hive/data/genomes/hbv1/hbv1.unmasked.2bit \ -workhorse=hgwdev -smallClusterHub=ku hbv1) > do.log 2>&1 # real 1m6.607s cat fb.hbv1.cpgIslandExtUnmasked.txt # 396 bases of 3182 (12.445%) in intersection ############################################################################# # cytoBandIdeo - (TBD - 2017-05-10 - Hiram) mkdir /hive/data/genomes/hbv1/bed/cytoBand cd /hive/data/genomes/hbv1/bed/cytoBand makeCytoBandIdeo.csh hbv1 ######################################################################### # ucscToINSDC and ucscToRefSeq table/track (DONE - 2017-06-02 - Hiram) # really simple situation here, only one name to deal with mkdir /hive/data/genomes/hbv1/bed/ucscToINSDC cd /hive/data/genomes/hbv1/bed/ucscToINSDC # lookup the INSDC name at: # https://www.ncbi.nlm.nih.gov/genome/5536 printf "NC_003977v2\t0\t3182\tNC_003977.2\n" > ucscToRefSeq.bed printf "NC_003977v2\t0\t3182\tV01460.1\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 hbv1 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 hbv1 ucscToRefSeq ./ucscToRefSeq.sql ucscToRefSeq.bed # checkTableCoords should be silent checkTableCoords hbv1 # each should cover %100 entirely: featureBits -countGaps hbv1 ucscToINSDC # 3182 bases of 3182 (100.000%) in intersection featureBits -countGaps hbv1 ucscToRefSeq # 3182 bases of 3182 (100.000%) in intersection ######################################################################### # add chromAlias table (DONE - 2017-06-02 - Hiram) mkdir /hive/data/genomes/hbv1/bed/chromAlias cd /hive/data/genomes/hbv1/bed/chromAlias hgsql -N -e 'select chrom,name,"refseq" from ucscToRefSeq;' hbv1 \ > ucsc.refseq.tab hgsql -N -e 'select chrom,name,"genbank" from ucscToINSDC;' hbv1 \ > ucsc.genbank.tab awk '{printf "%s\t%s\t%s\n", $2,$1,$3}' ucsc.genbank.tab ucsc.refseq.tab \ | sort > hbv1.chromAlias.tab cat hbv1.chromAlias.tab # NC_003977.2 NC_003977v2 refseq # V01460.1 NC_003977v2 genbank hgLoadSqlTab hbv1 chromAlias ~/kent/src/hg/lib/chromAlias.sql \ hbv1.chromAlias.tab ######################################################################### # fixup search rule for assembly track/gold table (DONE - 2017-06-02 - Hiram) cd ~/kent/src/hg/makeDb/trackDb/HBV/hbv1 # preview prefixes and suffixes: hgsql -N -e "select frag from gold;" hbv1 \ | sed -e 's/[0-9][0-9]*//;' | sort | uniq -c # 1 NC_.2 # 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;" hbv1 | wc -l # 1 hgsql -N -e "select frag from gold;" hbv1 \ | egrep -e 'NC_[0-9]+(\.[0-9]+)?' | wc -l # 1 hgsql -N -e "select frag from gold;" hbv1 \ | egrep -v -e 'NC_[0-9]+(\.[0-9]+)?' | wc -l # 0 # hence, add to trackDb/chicken/hbv1/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 - 2017-06-02 - Hiram) # RepeatMasker doesn't know about this virus sequence name as is, # scientificName # 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/hbv1/bed/repeatMasker cd /hive/data/genomes/hbv1/bed/repeatMasker time (doRepeatMasker.pl -buildDir=`pwd` \ -species "viruses" -bigClusterHub=ku -dbHost=hgwdev -workhorse=hgwdev \ -smallClusterHub=ku hbv1) > do.log 2>&1 & # real 1m49.755s # there were no repeats identified # and it fails with an empty nestedRepeats file during load # help the doLoad step finish: ln -s `pwd`/hbv1.rmsk.2bit /hive/data/genomes/hbv1/hbv1.rmsk.2bit # continue with cleanUp: time (doRepeatMasker.pl -buildDir=`pwd` \ -species "viruses" -bigClusterHub=ku -dbHost=hgwdev -workhorse=hgwdev \ -continue=cleanup -smallClusterHub=ku hbv1) > cleanup.log 2>&1 & # real 0m4.284s 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; * ########################################################################## # running simple repeat (DONE - 2017-06-12 - Hiram) mkdir /hive/data/genomes/hbv1/bed/simpleRepeat cd /hive/data/genomes/hbv1/bed/simpleRepeat # using trf409 1 here (human == 6) time (doSimpleRepeat.pl -buildDir=`pwd` -bigClusterHub=ku \ -dbHost=hgwdev -workhorse=hgwdev -smallClusterHub=ku \ -trf409 1 hbv1) > do.log 2>&1 & # XXX - there are no simple repeats, empty result # real 0m12.596s ######################################################################### # CREATE MICROSAT TRACK (TBD - 2017-04-11 - Hiram) # XXX - there are no simple repeats ssh hgwdev mkdir /cluster/data/hbv1/bed/microsat cd /cluster/data/hbv1/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 hbv1 microsat microsat.bed # Read 213828 elements of size 4 from microsat.bed ########################################################################## ## WINDOWMASKER (DONE - 2017-06-02 - Hiram) mkdir /hive/data/genomes/hbv1/bed/windowMasker cd /hive/data/genomes/hbv1/bed/windowMasker time (doWindowMasker.pl -buildDir=`pwd` -workhorse=hgwdev \ -dbHost=hgwdev hbv1) > do.log 2>&1 # real 0m23.043s # there are no repeats identified, failed on the empty files # need to cleanup anyway: time (doWindowMasker.pl -buildDir=`pwd` -workhorse=hgwdev \ -continue=cleanup -dbHost=hgwdev hbv1) > cleanup.log 2>&1 ########################################################################## # masking 2bit file (DONE - 2017-06-02 - Hiram) cd /hive/data/genomes/hbv1 # there are no repeats to mask, simply use the unmasked sequence: cp -p hbv1.unmasked.2bit hbv1.2bit # reset the symlink rm /gbdb/hbv1/hbv1.2bit ln -s `pwd`/hbv1.2bit /gbdb/hbv1/hbv1.2bit ########################################################################## # run up idKeys files for ncbiRefSeq (DONE - 2017-06-02 - Hiram) mkdir /hive/data/genomes/hbv1/bed/idKeys cd /hive/data/genomes/hbv1/bed/idKeys time (doIdKeys.pl -buildDir=`pwd` hbv1) > do.log 2>&1 & # real 0m16.968s cat hbv1.keySignature.txt # 7106cf68a1a0bc7c463a30d0ef3b156d ########################################################################## # cpgIslands - (DONE - 2017-06-02 - Hiram) mkdir /hive/data/genomes/hbv1/bed/cpgIslands cd /hive/data/genomes/hbv1/bed/cpgIslands time (doCpgIslands.pl -dbHost=hgwdev -bigClusterHub=ku \ -workhorse=hgwdev -smallClusterHub=ku hbv1) > do.log 2>&1 & # real 1m6.348s cat fb.hbv1.cpgIslandExt.txt # 396 bases of 3182 (12.445%) in intersection ############################################################################## # genscan - (DONE - 2017-06-02 - Hiram) mkdir /hive/data/genomes/hbv1/bed/genscan cd /hive/data/genomes/hbv1/bed/genscan time (doGenscan.pl -buildDir=`pwd` -workhorse=hgwdev -dbHost=hgwdev \ -bigClusterHub=ku hbv1) > do.log 2>&1 & # real 1m52.046s cat fb.hbv1.genscan.txt # 1110 bases of 3182 (34.884%) in intersection cat fb.hbv1.genscanSubopt.txt # 1063 bases of 3182 (33.407%) in intersection ############################################################################# # augustus gene track (TBD - 2017-04-13 - Hiram) # XXX augustus can not do virus sequence mkdir /hive/data/genomes/hbv1/bed/augustus cd /hive/data/genomes/hbv1/bed/augustus time (doAugustus.pl -buildDir=`pwd` -bigClusterHub=ku \ -species=human -dbHost=hgwdev -workhorse=hgwdev hbv1) > do.log 2>&1 & # real 72m23.671s cat fb.hbv1.augustusGene.txt # 29811614 bases of 2318132242 (1.286%) in intersection ############################################################################## # Create kluster run files (TBD - 2017-04-13 - Hiram) # numerator is hbv1 gapless bases "real" as reported by: featureBits -noRandom -noHap hbv1 gap # 0 bases of 3182 (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 \( 3182 / 2861349177 \) \* 1024 # ( 3182 / 2861349177 ) * 1024 = 0.001139 # repMatch=1 produces 578 overused 11-mers $ repMatch=2 produces 0 overused 11-mers # ==> use -repMatch=2, do not need to mask anything cd /hive/data/genomes/hbv1 blat hbv1.2bit \ /dev/null /dev/null -tileSize=11 -makeOoc=jkStuff/hbv1.11.ooc \ -repMatch=2 # Wrote 0 overused 11-mers to jkStuff/hbv1.11.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;' hbv1 | 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 # Hepatitis B virus 5671 1 0 # Hepatitis B virus subtype adw 1 0 0 # edit etc/genbank.conf to add hbv1 at the end # hbv1 (Hepatitis B virus - Taxid: 10407) hbv1.serverGenome = /hive/data/genomes/hbv1/hbv1.2bit hbv1.clusterGenome = /hive/data/genomes/hbv1/hbv1.2bit hbv1.ooc = /hive/data/genomes/hbv1/jkStuff/hbv1.11.ooc hbv1.lift = no hbv1.downloadDir = hbv1 hbv1.perChromTables = no hbv1.refseq.mrna.native.pslCDnaFilter = ${finished.refseq.mrna.native.pslCDnaFilter} hbv1.refseq.mrna.xeno.pslCDnaFilter = ${finished.refseq.mrna.xeno.pslCDnaFilter} hbv1.genbank.mrna.native.pslCDnaFilter = ${finished.genbank.mrna.native.pslCDnaFilter} hbv1.genbank.mrna.xeno.pslCDnaFilter = ${finished.genbank.mrna.xeno.pslCDnaFilter} hbv1.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 # hbv1.upstreamGeneTbl = ensGene # hbv1.upstreamMaf = multiz9way /hive/data/genomes/hpv1/bed/multiz9way/species.list git commit -m 'adding hbv1 Hepatitis B virus - refs #19533' etc/genbank.conf src/lib/gbGenome.c git push make etc-update make install-server cd /cluster/data/genbank time ./bin/gbAlignStep -initial hbv1 # logFile: var/build/logs/2017.06.03-09:54:08.hbv1.initalign.log # real 406m38.235s tail -2 var/build/logs/2017.06.03-09:54:08.hbv1.initalign.log hgwdev 2017.06.03-16:38:15 hbv1.initalign: Succeeded: hbv1 hgwdev 2017.06.03-16:40:47 hbv1.initalign: finish # logFile: var/build/logs/2017.06.02-11:29:04.hbv1.initalign.log # real 248m27.891s tail -2 var/build/logs/2017.06.02-11:29:04.hbv1.initalign.log # hgwdev 2017.06.02-15:37:28 hbv1.initalign: Succeeded: hbv1 # hgwdev 2017.06.02-15:37:32 hbv1.initalign: finish # To re-do, rm the dir first: # /cluster/data/genbank/work/initial.hbv1 # load database when finished ssh hgwdev cd /cluster/data/genbank time ./bin/gbDbLoadStep -drop -initialLoad hbv1 # logFile: var/dbload/hgwdev/logs/2017.06.06-08:35:26.hbv1.dbload.log # real 136m30.161s XXX - ready to continue - Wed Jun 7 12:41:23 PDT 2017 # logFile: logFile: var/dbload/hgwdev/logs/2017.06.02-16:56:52.hbv1.dbload.log # real 16m51.160s tail -1 var/dbload/hgwdev/logs/2017.06.02-16:56:52.hbv1.dbload.log # hgwdev 2017.06.02-17:13:43 hbv1.dbload: finish # to completely re-run with altered genbank.conf: cd /cluster/data/genbank/data/aligned og -d */hbv1 # drwxrwsr-x 49 4096 Jun 2 15:33 genbank.219.0/hbv1 # drwxrwsr-x 25 4096 Jun 2 15:37 refseq.82/hbv1 cd /cluster/data/genbank/data/aligned rm -fr */hbv1 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 hbv1 to: # etc/align.dbs etc/hgwdev.dbs git add etc/align.dbs etc/hgwdev.dbs git commit -m 'adding hbv1 to the update alignments refs #19228' etc/align.dbs etc/hgwdev.dbs git push make etc-update ############################################################################# # ncbiGene (TBD - 2017-05-10 - Hiram) mkdir /hive/data/genomes/hbv1/bed/ncbiGene cd /hive/data/genomes/hbv1/bed/ncbiGene # switching the names from column 1 to 12 and 12 to 1 with the awk: gff3ToGenePred -useName -attrsOut=hbv1.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]' > hbv1.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=hbv1 hbv1.ncbiGene.gp # checked: 7 failed: 0 hgLoadGenePred -genePredExt hbv1 ncbiGene hbv1.ncbiGene.gp genePredCheck -db=hbv1 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 ("hbv1", "blat1a", "17872", "1", "0"); \ INSERT INTO blatServers (db, host, port, isTrans, canPcr) \ VALUES ("hbv1", "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="hbv1";' 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=hbv1 -tableCoverage all.joiner joinerCheck -database=hbv1 -times all.joiner joinerCheck -database=hbv1 -keys all.joiner cd /hive/data/genomes/hbv1 time (makeDownloads.pl -workhorse=hgwdev hbv1) > downloads.log 2>&1 # real 22m35.669s # now ready for pushQ entry mkdir /hive/data/genomes/hbv1/pushQ cd /hive/data/genomes/hbv1/pushQ time (makePushQSql.pl -redmineList hbv1) \ > hbv1.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/hbv1/wib/gc5Base.wib # WARNING: hgwdev does not have /gbdb/hbv1/wib/quality.wib # WARNING: hgwdev does not have /gbdb/hbv1/bbi/quality.bw # WARNING: hbv1 does not have seq # WARNING: hbv1 does not have extFile # enter the path names to the redmine listings in the redmine issue # refs 19228 #########################################################################