# for emacs: -*- mode: sh; -*- # This file describes browser build for the staAur1 ######################################################################### # photo from WikiMedia Commons # (DONE - 2017-04-04 - Hiram) mkdir -p /hive/data/genomes/staAur1/photo cd /hive/data/genomes/staAur1/photo wget --timestamping \ "https://upload.wikimedia.org/wikipedia/commons/d/d3/Staphylococcus_aureus_VISA_2.jpg" convert -quality 80 -geometry 350x350 Staphylococcus_aureus_VISA_2.jpg \ Staphylococcus_aureus.jpg cd /hive/data/genomes/staAur1 printf 'photoCreditURL https://phil.cdc.gov/phil/details.asp?pid=11157 photoCreditName Centers for Disease Control and Prevention's Public Health Image Library ' > photoReference.txt cat photoReference.txt photoCreditURL https://phil.cdc.gov/phil/details.asp?pid=11157 photoCreditName Centers for Disease Control and Prevention's Public Health Image Library # Checking in that photograph to the source tree git commit -m 'Staphylococcus aureus from CDC public health image library refs #19937' Staphylococcus_aureus.jpg ######################################################################### # Initial steps (DONE - 2017-08-04 - Hiram) # This initialBuild.txt document was started from hpv1 # version of initialBuild.txt sed -e 's/hbv1/staAur1/g; s/DONE/TBD/g; s/Hbv1/StaAur1/g;' \ ../hbv1/initialBuild.txt > initialBuild.txt mkdir /hive/data/genomes/staAur1/refseq cd /hive/data/genomes/staAur1/refseq GCF_000013425.1_ASM1342v1 # bacteria/Staphylococcus_aureus/all_assembly_versions/GCF_000013425.1_ASM1342v1 export accession="GCF_000013425.1" export asmId="ASM1342v1" export level0="GCF" export level1="000" export level2="013" export level3="425" time rsync -L -a -P rsync://ftp.ncbi.nlm.nih.gov/genomes/all/$level0/$level1/$level2/$level3/${accession}_${asmId}/ ./ # sent 298 bytes received 5247197 bytes 1499284.29 bytes/sec # total size is 5244835 speedup is 1.00 # real 0m2.911s # check assembly size for later reference: faSize GCF*v1_genomic.fna.gz # 2821361 bases (1 N's 2821360 real 2821360 upper 0 lower) in 1 sequences in 1 files # this information is from the top of # staAur1/refseq/GCF_000013425.1_ASM1342v1_assembly_report.txt # Assembly name: ASM1342v1 # Organism name: Staphylococcus aureus subsp. aureus NCTC 8325 (firmicutes) # Infraspecific name: strain=NCTC 8325 # Taxid: 93061 # BioSample: SAMN02604235 # BioProject: PRJNA237 # Submitter: University of Oklahoma Health Sciences Center # Date: 2006-2-13 # Assembly type: n/a # Release type: major # Assembly level: Complete Genome # Genome representation: full # RefSeq category: Reference Genome # GenBank assembly accession: GCA_000013425.1 # RefSeq assembly accession: GCF_000013425.1 # RefSeq assembly and GenBank assemblies identical: yes # ## Assembly-Units: ## GenBank Unit Accession RefSeq Unit Accession Assembly-Unit name ## GCA_000013435.1 GCF_000013435.1 Primary Assembly ############################################################################# # establish config.ra file (DONE - Hiram - 2017-08-04) # arguments here are: cd /hive/data/genomes/staAur1 $HOME/kent/src/hg/utils/automation/prepConfig.pl staAur1 bacteria \ bacteria ./refseq/*_assembly_report.txt > staAur1.config.ra # going to need a mitoAcc ? # this clade 'bacteria' does not yet exist in hgcentraltest.clade hgsql hgcentraltest -e 'INSERT INTO clade (name, label, priority) VALUES ("bacteria", "Bacteria", 1500)' # fixup the genomeCladePriority to 1500 # fixup scientificName from: # scientificName Staphylococcus aureus subsp. aureus NCTC 8325 # to: # scientificName Staphylococcus aureus # fixup commonName from commonName Firmicutes to: Staph # set mitoAcc none # to see order keys to verify this one is correct: # hgsql -e 'select name,organism,orderKey from dbDb order by orderKey;' \ # hgcentraltest | less # saiBol1 Squirrel monkey 19725 # staAur1 19765 # conCri1 Star-nosed mole 19805 # verify it looks sane cat staAur1.config.ra # config parameters for makeGenomeDb.pl: db staAur1 clade bacteria genomeCladePriority 1500 scientificName Staphylococcus aureus commonName Staph assemblyDate Feb. 2006 assemblyLabel University of Oklahoma Health Sciences Center assemblyShortLabel ASM1342v1 orderKey 19765 mitoAcc none fastaFiles /hive/data/genomes/staAur1/ucsc/*.fa.gz agpFiles /hive/data/genomes/staAur1/ucsc/*.agp # qualFiles none dbDbSpeciesDir bacteria photoCreditURL https://phil.cdc.gov/phil/details.asp?pid=11157 photoCreditName Centers for Disease Control and Prevention's Public Health Image Library ncbiGenomeId 154 ncbiAssemblyId 34528 ncbiAssemblyName ASM1342v1 ncbiBioProject 237 ncbiBioSample SAMN02604235 genBankAccessionID GCF_000013425.1 taxId 93061 ############################################################################# # setup UCSC named files (DONE - 2017-08-04 - Hiram) mkdir /hive/data/genomes/staAur1/ucsc cd /hive/data/genomes/staAur1/ucsc # one simple sequence: zcat ../refseq/GCF_000013425.1_ASM1342v1_genomic.fna.gz \ | sed -e 's/^>NC_007795.1.*/>NC_007795v1/;' | gzip > chr.fa.gz printf "NC_007795v1\t1\t2821361\t1\tF\tNC_007795.1\t1\t2821361\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 - 2017-08-04 - Hiram) cd /hive/data/genomes/staAur1 # verify sequence and AGP are OK: time (makeGenomeDb.pl -workhorse=hgwdev -dbHost=hgwdev -fileServer=hgwdev \ -stop=agp staAur1.config.ra) > agp.log 2>&1 # real 0m8.712s # then finish it off: time (makeGenomeDb.pl -workhorse=hgwdev -dbHost=hgwdev \ -fileServer=hgwdev -continue=db staAur1.config.ra) > db.log 2>&1 # real 0m19.868s # check in the trackDb files created in TemporaryTrackDbCheckout/ # and add staAur1 to trackDb/makefile # temporary symlink until masked sequence is available cd /hive/data/genomes/staAur1 ln -s `pwd`/staAur1.unmasked.2bit /gbdb/staAur1/staAur1.2bit ############################################################################## # cpgIslands on UNMASKED sequence (DONE - 2017-08-04 - Hiram) mkdir /hive/data/genomes/staAur1/bed/cpgIslandsUnmasked cd /hive/data/genomes/staAur1/bed/cpgIslandsUnmasked time (doCpgIslands.pl -dbHost=hgwdev -bigClusterHub=ku -buildDir=`pwd` \ -tableName=cpgIslandExtUnmasked \ -maskedSeq=/hive/data/genomes/staAur1/staAur1.unmasked.2bit \ -workhorse=hgwdev -smallClusterHub=ku staAur1) > do.log 2>&1 # real 0m37.441s cat fb.staAur1.cpgIslandExtUnmasked.txt # 17793 bases of 2821361 (0.631%) in intersection ############################################################################# # cytoBandIdeo - (DONE - 2017-08-04 - Hiram) mkdir /hive/data/genomes/staAur1/bed/cytoBand cd /hive/data/genomes/staAur1/bed/cytoBand makeCytoBandIdeo.csh staAur1 ######################################################################### # ucscToINSDC and ucscToRefSeq table/track (DONE - 2017-08-05 - Hiram) # really simple situation here, only one name to deal with mkdir /hive/data/genomes/staAur1/bed/ucscToINSDC cd /hive/data/genomes/staAur1/bed/ucscToINSDC # lookup the Genbank/INSDC name at: # https://www.ncbi.nlm.nih.gov/assembly/GCA_000013425.1 # In this case: NC_007795.1 == CP000253.1 printf "NC_007795v1\t0\t2821361\tNC_007795.1\n" > ucscToRefSeq.bed printf "NC_007795v1\t0\t2821361\tCP000253.1\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 staAur1 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 staAur1 ucscToRefSeq ./ucscToRefSeq.sql ucscToRefSeq.bed # checkTableCoords should be silent checkTableCoords staAur1 # each should cover %100 entirely: featureBits -countGaps staAur1 ucscToINSDC # 2821361 bases of 2821361 (100.000%) in intersection featureBits -countGaps staAur1 ucscToRefSeq # 2821361 bases of 2821361 (100.000%) in intersection ######################################################################### # add chromAlias table (DONE - 2017-08-05 - Hiram) mkdir /hive/data/genomes/staAur1/bed/chromAlias cd /hive/data/genomes/staAur1/bed/chromAlias hgsql -N -e 'select chrom,name,"refseq" from ucscToRefSeq;' staAur1 \ > ucsc.refseq.tab hgsql -N -e 'select chrom,name,"genbank" from ucscToINSDC;' staAur1 \ > ucsc.genbank.tab awk '{printf "%s\t%s\t%s\n", $2,$1,$3}' ucsc.genbank.tab ucsc.refseq.tab \ | sort > staAur1.chromAlias.tab cat staAur1.chromAlias.tab | sed -e 's/^/# /;' # CP000253.1 NC_007795v1 genbank # NC_007795.1 NC_007795v1 refseq hgLoadSqlTab staAur1 chromAlias ~/kent/src/hg/lib/chromAlias.sql \ staAur1.chromAlias.tab ######################################################################### # fixup search rule for assembly track/gold table (DONE - 2017-08-05 - Hiram) cd ~/kent/src/hg/makeDb/trackDb/bacteria/staAur1 # preview prefixes and suffixes: hgsql -N -e "select frag from gold;" staAur1 \ | 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;" staAur1 | wc -l # 1 hgsql -N -e "select frag from gold;" staAur1 \ | egrep -e 'NC_[0-9]+(\.[0-9]+)?' | wc -l # 1 hgsql -N -e "select frag from gold;" staAur1 \ | egrep -v -e 'NC_[0-9]+(\.[0-9]+)?' | wc -l # 0 # hence, add to trackDb/bacteria/staAur1/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 - 2017-08-04 - Hiram) # RepeatMasker doesn't know about this virus sequence name as is, # scientificName Staphylococcus aureus # found this in taxonomy.dat table in RM: # 'low g+c gram-positive bacteria' name, taxId 1239 # from: /hive/data/staging/data/RepeatMasker140131/Libraries/taxonomy.dat mkdir /hive/data/genomes/staAur1/bed/repeatMasker cd /hive/data/genomes/staAur1/bed/repeatMasker time (doRepeatMasker.pl -buildDir=`pwd` \ -species "low g+c gram-positive bacteria" -bigClusterHub=ku \ -dbHost=hgwdev -workhorse=hgwdev \ -smallClusterHub=ku staAur1) > do.log 2>&1 & # real 1m49.755s # fails with an empty nestedRepeats file during load # help the doLoad step finish: ln -s `pwd`/staAur1.rmsk.2bit /hive/data/genomes/staAur1/staAur1.rmsk.2bit # continue with cleanUp: time (doRepeatMasker.pl -buildDir=`pwd` \ -species "low g+c gram-positive bacteria" -bigClusterHub=ku \ -dbHost=hgwdev -workhorse=hgwdev -continue=cleanup \ -smallClusterHub=ku staAur1) > cleanup.log 2>&1 & # real 0m4.496s 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; * cat faSize.rmsk.txt # 2821361 bases (1 N's 2821360 real 2807400 upper 13960 lower) in 1 sequences in 1 files # %0.49 masked total, %0.49 masked real time featureBits -countGaps staAur1 rmsk # 13960 bases of 2821361 (0.495%) in intersection # real 0m0.016s ########################################################################## # running simple repeat (DONE - 2017-08-04 - Hiram) mkdir /hive/data/genomes/staAur1/bed/simpleRepeat cd /hive/data/genomes/staAur1/bed/simpleRepeat # using trf409 1 here (human == 6) time (doSimpleRepeat.pl -buildDir=`pwd` -bigClusterHub=ku \ -dbHost=hgwdev -workhorse=hgwdev -smallClusterHub=ku \ -trf409 1 staAur1) > do.log 2>&1 & # real 0m24.338s cat fb.simpleRepeat # 26152 bases of 2821361 (0.927%) in intersection ######################################################################### # CREATE MICROSAT TRACK (DONE - 2017-08-04 - Hiram) # XXX - this makes an empty microsat.bed file, nothing to load ssh hgwdev mkdir /cluster/data/staAur1/bed/microsat cd /cluster/data/staAur1/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 staAur1 microsat microsat.bed ########################################################################## ## WINDOWMASKER (DONE - 2017-08-04 - Hiram) mkdir /hive/data/genomes/staAur1/bed/windowMasker cd /hive/data/genomes/staAur1/bed/windowMasker time (doWindowMasker.pl -buildDir=`pwd` -workhorse=hgwdev \ -dbHost=hgwdev staAur1) > do.log 2>&1 # real 0m31.476s cat faSize.staAur1.cleanWMSdust.txt # 2821361 bases (1 N's 2821360 real 2364826 upper 456534 lower) in 1 sequences in 1 files # %16.18 masked total, %16.18 masked real cat fb.staAur1.rmsk.windowmaskerSdust.txt # 8293 bases of 2821361 (0.294%) in intersection ########################################################################## # masking 2bit file (DONE - 2017-08-04 - Hiram) cd /hive/data/genomes/staAur1 twoBitMask staAur1.rmsk.2bit \ -add bed/simpleRepeat/trfMask.bed staAur1.rmsk.trf.2bit twoBitMask staAur1.rmsk.trf.2bit -type=.bed \ -add bed/windowMasker/cleanWMask.bed.gz staAur1.2bit twoBitToFa staAur1.2bit stdout | faSize stdin > faSize.staAur1.2bit.txt cat faSize.staAur1.2bit.txt # 2821361 bases (1 N's 2821360 real 2359001 upper 462359 lower) in 1 sequences in 1 files # %16.39 masked total, %16.39 masked real # reset the symlink rm /gbdb/staAur1/staAur1.2bit ln -s `pwd`/staAur1.2bit /gbdb/staAur1/staAur1.2bit ########################################################################## # run up idKeys files for ncbiRefSeq (DONE - 2017-08-04 - Hiram) mkdir /hive/data/genomes/staAur1/bed/idKeys cd /hive/data/genomes/staAur1/bed/idKeys time (doIdKeys.pl -buildDir=`pwd` staAur1) > do.log 2>&1 & # real 0m17.167s cat staAur1.keySignature.txt # 3d70b1f5bdeec2114c63b7ce2017ea96 ########################################################################## # cpgIslands - (DONE - 2017-08-04 - Hiram) mkdir /hive/data/genomes/staAur1/bed/cpgIslands cd /hive/data/genomes/staAur1/bed/cpgIslands time (doCpgIslands.pl -dbHost=hgwdev -bigClusterHub=ku \ -workhorse=hgwdev -smallClusterHub=ku staAur1) > do.log 2>&1 & # real 0m36.836s cat fb.staAur1.cpgIslandExt.txt # 16205 bases of 2821361 (0.574%) in intersection ############################################################################## # genscan - (DONE - 2017-08-04 - Hiram) mkdir /hive/data/genomes/staAur1/bed/genscan cd /hive/data/genomes/staAur1/bed/genscan time (doGenscan.pl -buildDir=`pwd` -workhorse=hgwdev -dbHost=hgwdev \ -bigClusterHub=ku staAur1) > do.log 2>&1 & # real 2m7.070s cat fb.staAur1.genscan.txt # 395771 bases of 2821361 (14.028%) in intersection cat fb.staAur1.genscanSubopt.txt # 104700 bases of 2821361 (3.711%) in intersection ############################################################################# # augustus gene track (TBD - 2017-04-13 - Hiram) # XXX augustus can not do bacteria sequence ? mkdir /hive/data/genomes/staAur1/bed/augustus cd /hive/data/genomes/staAur1/bed/augustus time (doAugustus.pl -buildDir=`pwd` -bigClusterHub=ku \ -species=human -dbHost=hgwdev -workhorse=hgwdev staAur1) > do.log 2>&1 & # real 72m23.671s cat fb.staAur1.augustusGene.txt # 29811614 bases of 2318132242 (1.286%) in intersection ############################################################################## # Create kluster run files (DONE - 2017-08-04 - Hiram) # numerator is staAur1 gapless bases "real" as reported by: featureBits -noRandom -noHap staAur1 gap # 0 bases of 2821361 (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 \( 2821361 / 2861349177 \) \* 1024 # ( 2821361 / 2861349177 ) * 1024 = 1.009689 # repMatch=1 produces 410921 overused 11-mers # repMatch=2 produces 73051 overused 11-mers # repMatch=3 produces 18919 overused 11-mers # repMatch=3 produces 6121 overused 11-mers # repMatch=5 produces 2319 overused 11-mers # repMatch=6 produces 923 overused 11-mers # repMatch=7 produces 379 overused 11-mers # repMatch=8 produces 168 overused 11-mers # repMatch=9 produces 80 overused 11-mers # repMatch=10 produces 43 overused 11-mers # ... # repMatch=20 produces 0 overused 11-mers # ==> use -repMatch=20, do not need to mask anything cd /hive/data/genomes/staAur1 blat staAur1.2bit \ /dev/null /dev/null -tileSize=11 -makeOoc=jkStuff/staAur1.11.ooc \ -repMatch=20 # Wrote 0 overused 11-mers to jkStuff/staAur1.11.ooc # check non-bridged gaps to see what the typical size is: # there are no gaps in this assembly: hgsql -N -e 'select bridge from gap;' staAur1 | sort | uniq -c # no output, nothing to see here ######################################################################### # GENBANK AUTO UPDATE (DONE - 2017-08-04 - Hiram) ssh hgwdev cd $HOME/kent/src/hg/makeDb/genbank git pull # /cluster/data/genbank/data/organism.lst shows: # organism mrnaCnt estCnt refSeqCnt # Staphylococcus 2 0 0 # Staphylococcus aureus 185 0 0 # Staphylococcus aureus subsp. aureus NCTC 8325 32 0 0 # Staphylococcus aureus subsp. aureus RN4220 1 0 0 # Staphylococcus epidermidis 46 1255 0 # Staphylococcus lentus 1 0 0 # Staphylococcus lugdunensis 9 0 0 # Staphylococcus phage phi-42 1 0 0 # Staphylococcus pseudintermedius 9 0 0 # Staphylococcus sp. B2_30 1 0 0 # Staphylococcus sp. B2_43 1 0 0 # Staphylococcus sp. SH24 1 0 0 # Staphylococcus warneri 1 0 0 # add these four to src/lib/gbGenome.c for staAurNames[] # Staphylococcus 2 0 0 # Staphylococcus aureus 185 0 0 # Staphylococcus aureus subsp. aureus NCTC 8325 32 0 0 # Staphylococcus aureus subsp. aureus RN4220 1 0 0 # edit etc/genbank.conf to add staAur1 just after aplCal1 and before hbv1 # staAur1 (Staphylococcus aureus - Taxid: 93061) staAur1.serverGenome = /hive/data/genomes/staAur1/staAur1.2bit staAur1.clusterGenome = /hive/data/genomes/staAur1/staAur1.2bit staAur1.ooc = /hive/data/genomes/staAur1/jkStuff/staAur1.11.ooc staAur1.lift = no staAur1.downloadDir = staAur1 staAur1.perChromTables = no staAur1.refseq.mrna.native.pslCDnaFilter = ${finished.refseq.mrna.native.pslCDnaFilter} staAur1.refseq.mrna.xeno.pslCDnaFilter = ${finished.refseq.mrna.xeno.pslCDnaFilter} staAur1.genbank.mrna.native.pslCDnaFilter = ${finished.genbank.mrna.native.pslCDnaFilter} staAur1.genbank.mrna.xeno.pslCDnaFilter = ${finished.genbank.mrna.xeno.pslCDnaFilter} staAur1.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 # staAur1.upstreamGeneTbl = ensGene # staAur1.upstreamMaf = multiz9way /hive/data/genomes/staAur1/bed/multiz9way/species.list git commit -m 'adding staAur1 Staphylococcus aureus- refs #19937' etc/genbank.conf src/lib/gbGenome.c git push make install-server make etc-update cd /cluster/data/genbank time ./bin/gbAlignStep -initial staAur1 # logFile: var/build/logs/2017.08.04-14:20:13.staAur1.initalign.log # real 296m21.433s tail -2 var/build/logs/2017.08.04-14:20:13.staAur1.initalign.log hgwdev 2017.08.04-19:16:28 staAur1.initalign: Succeeded: staAur1 hgwdev 2017.08.04-19:16:35 staAur1.initalign: finish # To re-do, rm the dir first: # /cluster/data/genbank/work/initial.staAur1 # load database when finished ssh hgwdev cd /cluster/data/genbank time ./bin/gbDbLoadStep -drop -initialLoad staAur1 # logFile: var/dbload/hgwdev/logs/2017.08.05-00:32:05.staAur1.dbload.log # real 19m45.284s # enable daily alignment and update of hgwdev cd ~/kent/src/hg/makeDb/genbank git pull # add staAur1 to: # etc/align.dbs etc/hgwdev.dbs git commit -m 'adding staAur1 to the update alignments refs #19337' etc/align.dbs etc/hgwdev.dbs git push make etc-update ############################################################################# # ncbiGene (DONE - 2017-08-05 - Hiram) mkdir /hive/data/genomes/staAur1/bed/ncbiGene cd /hive/data/genomes/staAur1/bed/ncbiGene # switching the names from column 1 to 12 and 12 to 1 with the awk: gff3ToGenePred -useName -attrsOut=staAur1.attrs.tab -geneNameAttr=gene \ ../../refseq/GCF_000013425.1_ASM1342v1_genomic.gff.gz \ stdout | sed -e 's/NC_007795.1/NC_007795v1/;' \ | awk -F'\t' '{print $12,$2,$3,$4,$5,$6,$7,$8,$9,$10,$11,$1,$13,$14,$15}' | tr '[ ]' '[\t]' > staAur1.ncbiGene.gp # rpmH NC_007795v1 - 2821009 2821147 2821009 2821147 1 2821009, # 2821147, 0 YP_501500.1 cmpl cmpl 0, # rnpA NC_007795v1 - 2820535 2820889 2820535 2820889 1 2820535, # 2820889, 0 YP_501499.1 cmpl cmpl 0, genePredCheck -db=staAur1 staAur1.ncbiGene.gp 2>&1 | sed -e 's/^/ # /;' # checked: 2844 failed: 0 hgLoadGenePred -genePredExt staAur1 ncbiGene staAur1.ncbiGene.gp genePredCheck -db=staAur1 ncbiGene 2>&1 | sed -e 's/^/ # /;' # checked: 2844 failed: 0 XXX - need to get gene descriptions out of the genbank record ######################################################################### # BLATSERVERS ENTRY (DONE - 2017-08-07 - 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 ("staAur1", "blat1a", "17876", "1", "0"); \ INSERT INTO blatServers (db, host, port, isTrans, canPcr) \ VALUES ("staAur1", "blat1a", "17877", "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="staAur1";' 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=staAur1 -tableCoverage all.joiner joinerCheck -database=staAur1 -times all.joiner joinerCheck -database=staAur1 -keys all.joiner cd /hive/data/genomes/staAur1 # needed a symlink for RM output: cd NC_007795v1 ln -s ../bed/repeatMasker/staAur1.sorted.fa.out NC_007795v1.fa.out cd .. time (makeDownloads.pl -workhorse=hgwdev staAur1) > downloads.log 2>&1 # real 0m12.888s # now ready for pushQ entry mkdir /hive/data/genomes/staAur1/pushQ cd /hive/data/genomes/staAur1/pushQ time (makePushQSql.pl -redmineList staAur1) \ > staAur1.pushQ.sql 2> stderr.out # real 3m37.776s # check for errors in stderr.out, some are OK, e.g.: # writing redmine listings to # redmine.staAur1.file.list # redmine.staAur1.table.list # redmine.staAur1.releaseLog.txt # WARNING: staAur1 does not have augustusGene # WARNING: staAur1 does not have microsat # WARNING: staAur1 does not have nestedRepeats # WARNING: staAur1 does not have seq # WARNING: staAur1 does not have extFile # WARNING: staAur1 does not have estOrientInfo # WARNING: Could not tell (from trackDb, all.joiner and hardcoded lists of # supporting and genbank tables) which tracks to assign these tables to: # ncbiGene # enter the path names to the redmine listings in the redmine issue # refs 19937 #########################################################################