# for emacs: -*- mode: sh; -*- # This file describes browser build for the aquChr2 # Golden eagle - Aquila chrysaetos canadensis # Assembly Name: Aquila_chrysaetos-1.0.2 # Organism name: Aquila chrysaetos canadensis # Taxid: 216574 # Submitter: The Genome Institute - Washington University School of # Medicine # Date: 2014-10-14 # BioSample: SAMN03079786 # Assembly type: haploid # Release type: major # Assembly level: Scaffold # Genome representation: full # GenBank Assembly Accession: GCA_000766835.1 (species-representative latest) # ## Assembly-Units: ## GenBank Unit Accession RefSeq Unit Accession Assembly-Unit name ## GCA_000766845.1 Primary Assembly # there is no chrMt sequence in this release or in NCBI nucleotide ############################################################################# # fetch sequence from new style download directory (DONE - 2015-03-04 - Hiram) # NCBI has redesigned their FTP download site, new type of address # and naming scheme mkdir -p /hive/data/genomes/aquChr2/genbank cd /hive/data/genomes/aquChr2/genbank time rsync -L -a -P \ rsync://ftp.ncbi.nlm.nih.gov/genomes/genbank/vertebrate_other/Aquila_chrysaetos/all_assembly_versions/GCA_000766835.1_Aquila_chrysaetos-1.0.2/ ./ # sent 280 bytes received 737708839 bytes 13535947.14 bytes/sec # total size is 737617040 speedup is 1.00 # real 0m53.748s # measure what we have here: faSize GCA_000766835.1_Aquila_chrysaetos-1.0.2_genomic.fna.gz # 1192725744 bases (12708611 N's 1180017133 real 962614476 upper # 217402657 lower) in 1141 sequences in 1 files # Total size: mean 1045333.7 sd 3203065.9 min 913 (JRUM01016734.1) # max 30727332 (KN265652.1) median 5587 # %18.23 masked total, %18.42 masked real # that top-level file is the same as the unplaced scaffold file: faSize GCA_000766835.1_Aquila_chrysaetos-1.0.2_assembly_structure/Primary_Assembly/unplaced_scaffolds/FASTA/unplaced.scaf.fna.gz # 1192725744 bases (12708611 N's 1180017133 real 1180017133 upper 0 lower) # in 1141 sequences in 1 files # Total size: mean 1045333.7 sd 3203065.9 min 913 (JRUM01016734.1) # max 30727332 (KN265652.1) median 5587 ############################################################################# # fixup to UCSC naming scheme (DONE - 2015-03-05 - Hiram) mkdir /hive/data/genomes/aquChr2/ucsc cd /hive/data/genomes/aquChr2/ucsc # since this is a scaffold-only assembly, merely use the accession names # and since there are all .1 versions, this sed statement will make them # all v1 version names: zcat ../genbank/GCA_000766835.1_Aquila_chrysaetos-1.0.2_assembly_structure/Primary_Assembly/unplaced_scaffolds/AGP/unplaced.scaf.agp.gz \ | grep -v "^#" | sed -e 's/\.1/v1/;' > chrUn.aquChr2.agp zcat ../genbank/GCA_000766835.1_Aquila_chrysaetos-1.0.2_assembly_structure/Primary_Assembly/unplaced_scaffolds/FASTA/unplaced.scaf.fna.gz \ | sed -e 's/.1 Aquila .*/v1/;' > chrUn.aquChr2.fa # verify these two files are compatible: faToTwoBit chrUn.aquChr2.fa test.2bit checkAgpAndFa chrUn.aquChr2.agp test.2bit 2>&1 | tail # All AGP and FASTA entries agree - both files are valid ############################################################################# # Initial database build (DONE - 2015-03-05 - Hiram) cd /hive/data/genomes/aquChr2 cat << '_EOF_' > aquChr2.config.ra # Config parameters for makeGenomeDb.pl: db aquChr2 clade vertebrate genomeCladePriority 50 scientificName Aquila chrysaetos canadensis commonName Golden eagle assemblyDate Oct. 2014 assemblyLabel WashU assemblyShortLabel aquChr-1.0.2 orderKey 7664 mitoAcc none fastaFiles /hive/data/genomes/aquChr2/ucsc/*.fa agpFiles /hive/data/genomes/aquChr2/ucsc/*.agp # qualFiles none dbDbSpeciesDir birds photoCreditURL http://commons.wikimedia.org/wiki/User:Juan_lacruz photoCreditName Juan Lacruz - Wikimedia Commons ncbiGenomeId 32031 ncbiAssemblyId 217061 ncbiAssemblyName Aquila_chrysaetos-1.0.2 ncbiBioProject 256103 genBankAccessionID GCA_000766835.1 taxId 216574 '_EOF_' # << happy emacs # verify sequence and AGP are OK: time (makeGenomeDb.pl -workhorse=hgwdev -dbHost=hgwdev -fileServer=hgwdev \ -stop=agp aquChr2.config.ra) > agp.log 2>&1 # *** All done! (through the 'agp' step) # real 11m27.166s # then finish it off: time (makeGenomeDb.pl -workhorse=hgwdev -dbHost=hgwdev \ -fileServer=hgwdev -continue=db aquChr2.config.ra) > db.log 2>&1 # real 105m22.277s # missing .jpg image in htdocs/images, continuing: time (makeGenomeDb.pl -workhorse=hgwdev -dbHost=hgwdev \ -fileServer=hgwdev -continue=trackDb aquChr2.config.ra) \ > trackDb.log 2>&1 # check in the trackDb files created and add to trackDb/makefile ########################################################################## # running repeat masker (DONE - 2015-03-05 - Hiram) mkdir /hive/data/genomes/aquChr2/bed/repeatMasker cd /hive/data/genomes/aquChr2/bed/repeatMasker time (doRepeatMasker.pl -buildDir=`pwd` \ -bigClusterHub=ku -dbHost=hgwdev -workhorse=hgwdev \ -smallClusterHub=ku aquChr2) > do.log 2>&1 # real 60m12.037s cat faSize.rmsk.txt # 1192725744 bases (12708611 N's 1180017133 real 1116967561 upper # 63049572 lower) in 1141 sequences in 1 files # Total size: mean 1045333.7 sd 3203065.9 min 913 (JRUM01016734v1) # max 30727332 (KN265652v1) median 5587 # %5.29 masked total, %5.34 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 aquChr2 rmsk # 63129821 bases of 1192725744 (5.293%) in intersection # real 0m6.633s # why is it different than the faSize above ? # because rmsk masks out some N's as well as bases, the count above # separates out the N's from the bases, it doesn't show lower case N's ########################################################################## # running simple repeat (DONE - 2015-03-05 - Hiram) mkdir /hive/data/genomes/aquChr2/bed/simpleRepeat cd /hive/data/genomes/aquChr2/bed/simpleRepeat time (doSimpleRepeat.pl -buildDir=`pwd` -bigClusterHub=ku \ -dbHost=hgwdev -workhorse=hgwdev -smallClusterHub=ku \ aquChr2) > do.log 2>&1 # real 5m53.811s cat fb.simpleRepeat # 7586715 bases of 1180019022 (0.643%) in intersection # using the Window Masker result: cd /hive/data/genomes/aquChr2 twoBitMask bed/windowMasker/aquChr2.cleanWMSdust.2bit \ -add bed/simpleRepeat/trfMask.bed aquChr2.2bit # you can safely ignore the warning about fields >= 13 twoBitToFa aquChr2.2bit stdout | faSize stdin > faSize.aquChr2.2bit.txt cat faSize.aquChr2.2bit.txt # 1192725744 bases (12708611 N's 1180017133 real 956431179 upper # 223585954 lower) in 1141 sequences in 1 files # Total size: mean 1045333.7 sd 3203065.9 min 913 (JRUM01016734v1) # max 30727332 (KN265652v1) median 5587 # %18.75 masked total, %18.95 masked real rm /gbdb/aquChr2/aquChr2.2bit ln -s `pwd`/aquChr2.2bit /gbdb/aquChr2/aquChr2.2bit ########################################################################## # CREATE MICROSAT TRACK (DONE - 2015-06-22 - Hiram) ssh hgwdev mkdir /cluster/data/aquChr2/bed/microsat cd /cluster/data/aquChr2/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 aquChr2 microsat microsat.bed # Read 1314 elements of size 4 from microsat.bed ########################################################################## ## WINDOWMASKER (DONE - 2015-03-05 - Hiram) mkdir /hive/data/genomes/aquChr2/bed/windowMasker cd /hive/data/genomes/aquChr2/bed/windowMasker time (doWindowMasker.pl -buildDir=`pwd` -workhorse=hgwdev \ -dbHost=hgwdev aquChr2) > do.log 2>&1 # real 688m38.613s # most interesting very long run time for this small genome ? # Masking statistics cat faSize.aquChr2.cleanWMSdust.txt # 1192725744 bases (12708611 N's 1180017133 real 956589777 upper # 223427356 lower) in 1141 sequences in 1 files # Total size: mean 1045333.7 sd 3203065.9 min 913 (JRUM01016734v1) # max 30727332 (KN265652v1) median 5587 # %18.73 masked total, %18.93 masked real cat fb.aquChr2.rmsk.windowmaskerSdust.txt # 37125217 bases of 1192725744 (3.113%) in intersection ########################################################################## # cpgIslands - (DONE - 2015-03-06 - Hiram) mkdir /hive/data/genomes/aquChr2/bed/cpgIslands cd /hive/data/genomes/aquChr2/bed/cpgIslands time (doCpgIslands.pl -dbHost=hgwdev -bigClusterHub=ku \ -workhorse=hgwdev -smallClusterHub=ku aquChr2) > do.log 2>&1 & # real 2m11.511s cat fb.aquChr2.cpgIslandExt.txt # 23426181 bases of 1180019022 (1.985%) in intersection ############################################################################## # cpgIslands on UNMASKED sequence (DONE - 2015-03-05 - Hiram) mkdir /hive/data/genomes/aquChr2/bed/cpgIslandsUnmasked cd /hive/data/genomes/aquChr2/bed/cpgIslandsUnmasked time (doCpgIslands.pl -dbHost=hgwdev -bigClusterHub=ku -buildDir=`pwd` \ -tableName=cpgIslandExtUnmasked \ -maskedSeq=/hive/data/genomes/aquChr2/aquChr2.unmasked.2bit \ -workhorse=hgwdev -smallClusterHub=ku aquChr2) > do.log 2>&1 # real 4m9.741s cat fb.aquChr2.cpgIslandExtUnmasked.txt # 30797471 bases of 1180019022 (2.610%) in intersection ############################################################################# # cytoBandIdeo - (DONE - 2015-03-05 - Hiram) mkdir /hive/data/genomes/aquChr2/bed/cytoBand cd /hive/data/genomes/aquChr2/bed/cytoBand makeCytoBandIdeo.csh aquChr2 ######################################################################### # genscan - (DONE - 2015-03-06 - Hiram) mkdir /hive/data/genomes/aquChr2/bed/genscan cd /hive/data/genomes/aquChr2/bed/genscan time (doGenscan.pl -buildDir=`pwd` -workhorse=hgwdev -dbHost=hgwdev \ -bigClusterHub=ku aquChr2) > do.log 2>&1 # real 9m58.844s # Completed: 1140 of 1141 jobs # Crashed: 1 jobs # CPU time in finished jobs: 28452s 474.20m 7.90h 0.33d 0.001 y # IO & Wait Time: 5894s 98.23m 1.64h 0.07d 0.000 y # Average job time: 30s 0.50m 0.01h 0.00d # Longest finished job: 780s 13.00m 0.22h 0.01d # Submission to last job: 782s 13.03m 0.22h 0.01d # one job failed, it passed with a window size of 2,000,000 time (doGenscan.pl -buildDir=`pwd` -workhorse=hgwdev -dbHost=hgwdev \ -continue=makeBed -bigClusterHub=ku aquChr2) > makeBed.log 2>&1 # real 3m7.584s cat fb.aquChr2.genscan.txt # 26595865 bases of 1180019022 (2.254%) in intersection cat fb.aquChr2.genscanSubopt.txt # 30584112 bases of 1180019022 (2.592%) in intersection ######################################################################## # Create kluster run files (DONE - 2015-03-06 - Hiram) cd /hive/data/genomes/aquChr2 # numerator is aquChr2 gapless bases "real" as reported by: head -1 faSize.aquChr2.2bit.txt # 1192725744 bases (12708611 N's 1180017133 real 956431179 upper # 223585954 lower) in 1141 sequences in 1 files # numerator is 'real' base count # 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 \( 1180017133 / 2861349177 \) \* 1024 # ( 1180017133 / 2861349177 ) * 1024 = 422.296431 # ==> use -repMatch=400 according to size scaled down from 1024 for human. # and rounded down to nearest 50 cd /hive/data/genomes/aquChr2 time blat aquChr2.2bit \ /dev/null /dev/null -tileSize=11 -makeOoc=jkStuff/aquChr2.11.ooc \ -repMatch=400 # Wrote 15307 overused 11-mers to jkStuff/aquChr2.11.ooc # real 0m56.863s # there are no non-bridged gaps, do not need to do this # check non-bridged gaps to see what the typical size is: # hgsql -N -e 'select * from gap where bridge="no" order by size;' aquChr2 # | ave -tableOut -col=7 stdin # # min Q1 median Q3 max mean N sum stddev # 50076 58368.8 70128 100495 1.07816e+07 178173 670 1.19376e+08 672006 # note the minimum non-bridged gap size is 50,076 # gapToLift -verbose=2 -minGap=50000 aquChr2 jkStuff/aquChr2.nonBridged.lft \ # -bedFile=jkStuff/aquChr2.nonBridged.bed # hgsql -N \ # -e 'select * from gap where bridge="no" order by size;' aquChr2 \ # | ave -col=7 stdin # not needed: # gapToLift -verbose=2 -minGap=100 bosTau7 jkStuff/nonBridged.lft \ # -bedFile=jkStuff/nonBridged.bed # survey sizes: n50.pl chrom.sizes # reading: chrom.sizes # contig count: 1141, total size: 1192725744, one half size: 596362872 # cumulative N50 count contig contig size # 588589064 39 KN265690v1 9497852 # 596362872 one half size # 597819807 40 KN265691v1 9230743 ############################################################################# # GENBANK AUTO UPDATE (DONE - 2015-02-20 - Hiram) ssh hgwdev cd $HOME/kent/src/hg/makeDb/genbank git pull # /cluster/data/genbank/data/organism.lst shows: # #organism mrnaCnt estCnt refSeqCnt # Aquila chrysaetos canadensis - there are no entries at all # edit etc/genbank.conf to add aquChr2 just after melGal1 # aquChr2 (golden eagle) aquChr2.serverGenome = /hive/data/genomes/aquChr2/aquChr2.2bit aquChr2.clusterGenome = /hive/data/genomes/aquChr2/aquChr2.2bit aquChr2.ooc = /hive/data/genomes/aquChr2/jkStuff/aquChr2.11.ooc aquChr2.lift = no aquChr2.perChromTables = no aquChr2.refseq.mrna.xeno.pslCDnaFilter = ${lowCover.refseq.mrna.xeno.pslCDnaFilter} aquChr2.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter} aquChr2.genbank.mrna.xeno.pslCDnaFilter = ${lowCover.genbank.mrna.xeno.pslCDnaFilter} aquChr2.genbank.est.native.pslCDnaFilter = ${lowCover.genbank.est.native.pslCDnaFilter} aquChr2.genbank.est.xeno.pslCDnaFilter = ${lowCover.genbank.est.xeno.pslCDnaFilter} aquChr2.downloadDir = aquChr2 aquChr2.refseq.mrna.native.load = no aquChr2.refseq.mrna.xeno.load = yes aquChr2.refseq.mrna.xeno.loadDesc = yes aquChr2.genbank.mrna.native.load = no aquChr2.genbank.mrna.native.loadDesc = no aquChr2.genbank.mrna.xeno.load = yes aquChr2.genbank.mrna.xeno.loadDesc = yes aquChr2.genbank.est.native.load = no aquChr2.genbank.est.native.loadDesc = no # aquChr2.upstreamGeneTbl = ensGene git commit -m "Added aquChr2; refs #14560" etc/genbank.conf git push # update /cluster/data/genbank/: make etc-update # Edit src/lib/gbGenome.c to add new species. git commit -m "Added aquChr Aquila chrysaetos canadensis refs #14560" \ src/lib/gbGenome.c git push make install-server screen # control this business with a screen since it takes a while cd /cluster/data/genbank time ./bin/gbAlignStep -initial aquChr2 # logFile: var/build/logs/2015.03.06-14:45:22.aquChr2.initalign.log # real 391m48.657s # To re-do, rm the dir first: # /cluster/data/genbank/work/initial.aquChr2 # load database when finished ssh hgwdev cd /cluster/data/genbank time ./bin/gbDbLoadStep -drop -initialLoad aquChr2 # logFile: var/dbload/hgwdev/logs/2015.03.06-21:54:48.aquChr2.dbload.log # finished by brian after a loading problem: cat var/dbload/hgwdev/logs/2015.04.06-11:17:31.aquChr2.dbload.log # hgwdev 2015.04.06-11:17:31 aquChr2.dbload: begin # hgwdev 2015.04.06-11:17:31 aquChr2.dbload: command: bin/gbDbLoadStep -initialLoad -drop aquChr2 # gbLoadRna: selected genbank.206.0 aquChr2 xeno mrna: delete=0 seqChg=0 metaChg=0 extChg=0 new=21251711 orphan=0 derived=0 noChg=0 # gbLoadRna: selected refseq.69 aquChr2 xeno mrna: delete=0 seqChg=0 metaChg=0 extChg=0 new=431136 orphan=0 derived=0 noChg=0 # hgwdev 2015.04.06-13:07:41 aquChr2.dbload: finish # enable daily alignment and update of hgwdev cd ~/kent/src/hg/makeDb/genbank git pull # add aquChr2 to: # vi etc/align.dbs etc/hgwdev.dbs git commit -m "Added aquChr2 - Golden Eagle refs #15096" \ etc/align.dbs etc/hgwdev.dbs git push make etc-update ######################################################################### # ucscToRefSeq table/track (DONE - 2017-03-13 - Hiram) cut -f1 ../../chrom.sizes | sed -e 's/v1//;' \ | awk '{printf "%sv1\t%s.1\n", $1, $1}' | sort > ucscToINSDC.txt awk '{printf "%s\t%s\n", $2, $1}' ucscToINSDC.txt | sort > insdcToUcsc.txt grep -v "^#" ../../refseq/GCF*_assembly_report.txt | cut -f5,7 \ | awk '{printf "%s\t%s\n", $2, $1}' | sort > refseq.insdc.txt awk '{printf "%s\t0\t%d\n", $1,$2}' ../../chrom.sizes \ | sort > ucsc.coordinate.tab sort -k2 refseq.insdc.txt \ | join -1 2 -2 2 - ucscToINSDC.txt | sort -k3 \ | join -2 3 ucsc.coordinate.tab - | tr '[ ]' '[\t]' | cut -f1-4 \ > ucscToINSDC.bed sort -k2 refseq.insdc.txt \ | join -1 2 -2 2 - ucscToINSDC.txt | sort -k3 \ | join -2 3 ucsc.coordinate.tab - | tr '[ ]' '[\t]' | cut -f1-3,5 \ > ucscToRefSeq.bed # this UCSC assembly is missing the RefSeq chrM sequence: wc -l * # 1141 insdcToUcsc.txt # 1142 refseq.insdc.txt # 1141 ucsc.coordinate.tab # 1141 ucscToINSDC.bed # 1141 ucscToINSDC.txt # 1141 ucscToRefSeq.bed export chrSize=`cut -f1 ucscToRefSeq.bed | awk '{print length($0)}' | sort -n | tail -1` echo $chrSize # 14 sed -e "s/21/$chrSize/" $HOME/kent/src/hg/lib/ucscToINSDC.sql \ | sed -e 's/INSDC/RefSeq/g;' > ucscToRefSeq.sql hgLoadSqlTab aquChr2 ucscToRefSeq ./ucscToRefSeq.sql ucscToRefSeq.bed # checkTableCoords should be silent checkTableCoords aquChr2 # each should cover %100 entirely: featureBits -countGaps aquChr2 ucscToINSDC # 1192725744 bases of 1192725744 (100.000%) in intersection featureBits -countGaps aquChr2 ucscToRefSeq # 1192725744 bases of 1192725744 (100.000%) in intersection ######################################################################### # ucscToINSDC table/track (DONE - 2015-03-06 - Hiram) mkdir /hive/data/genomes/aquChr2/bed/ucscToINSDC cd /hive/data/genomes/aquChr2/bed/ucscToINSDC ~/kent/src/hg/utils/automation/ucscToINSDC.sh ~/kent/src/hg/utils/automation/ucscToINSDC.sh \ ../../genbank/GCA_*assembly_structure/Primary_Assembly awk '{printf "%s\t0\t%d\n", $1,$2}' ../../chrom.sizes \ | sort > name.coordinate.tab join name.coordinate.tab ucscToINSDC.txt | tr '[ ]' '[\t]' \ > ucscToINSDC.bed # verify all names are coming through, should be same line count: wc -l * # 1141 name.coordinate.tab # 1141 ucscToINSDC.bed # 1141 ucscToINSDC.txt cut -f1 ucscToINSDC.bed | awk '{print length($0)}' | sort -n | tail -1 # 14 # use the 14 in this sed sed -e "s/21/14/" $HOME/kent/src/hg/lib/ucscToINSDC.sql \ | hgLoadSqlTab aquChr2 ucscToINSDC stdin ucscToINSDC.bed checkTableCoords aquChr2 # should cover %100 entirely: featureBits -countGaps aquChr2 ucscToINSDC # 1192725744 bases of 1192725744 (100.000%) in intersection ######################################################################### # add chromAlias table (DONE - 2017-03-13 - Hiram) mkdir /hive/data/genomes/aquChr2/bed/chromAlias cd /hive/data/genomes/aquChr2/bed/chromAlias hgsql -N -e 'select chrom,name,"refseq" from ucscToRefSeq;' aquChr2 \ > ucsc.refseq.tab hgsql -N -e 'select chrom,name,"genbank" from ucscToINSDC;' aquChr2 \ > ucsc.genbank.tab awk '{printf "%s\t%s\t%s\n", $2,$1,$3}' ucsc.genbank.tab ucsc.refseq.tab \ | sort > aquChr2.chromAlias.tab hgLoadSqlTab aquChr2 chromAlias ~/kent/src/hg/lib/chromAlias.sql \ aquChr2.chromAlias.tab ######################################################################### # fixup search rule for assembly track/gold table (DONE - 2015-03-06 - Hiram) hgsql -N -e "select frag from gold;" aquChr2 | sort | head -1 JRUM01000001.1 hgsql -N -e "select frag from gold;" aquChr2 | sort | tail -2 JRUM01017030.1 JRUM01017031.1 # verify this rule will find them all or eliminate them all: hgsql -N -e "select frag from gold;" aquChr2 | wc -l # 17031 hgsql -N -e "select frag from gold;" aquChr2 \ | egrep -e 'JRUM010[0-9]+(\.1)?' | wc -l # 17031 hgsql -N -e "select frag from gold;" aquChr2 \ | egrep -v -e 'JRUM010[0-9]+(\.1)?' | wc -l # 0 # hence, add to trackDb/tarsier/aquChr2/trackDb.ra searchTable gold shortCircuit 1 termRegex JRUM010[0-9]+(\.1)? query select chrom,chromStart,chromEnd,frag from %s where frag like '%s%%' searchPriority 8 ######################################################################### # all.joiner update, downloads and in pushQ - (DONE 2015-04-14 - Hiram) cd $HOME/kent/src/hg/makeDb/schema # fixup all.joiner until this is a clean output joinerCheck -database=aquChr2 -tableCoverage all.joiner joinerCheck -database=aquChr2 -times all.joiner joinerCheck -database=aquChr2 -keys all.joiner cd /hive/data/genomes/aquChr2 time makeDownloads.pl aquChr2 > downloads.log 2>&1 # real 9m21.198s # now ready for pushQ entry mkdir /hive/data/genomes/aquChr2/pushQ cd /hive/data/genomes/aquChr2/pushQ makePushQSql.pl aquChr2 > aquChr2.pushQ.sql 2> stderr.out # check for errors in stderr.out, some are OK, e.g.: # WARNING: hgwdev does not have /gbdb/aquChr2/wib/gc5Base.wib # WARNING: hgwdev does not have /gbdb/aquChr2/wib/quality.wib # WARNING: hgwdev does not have /gbdb/aquChr2/bbi/qualityBw/quality.bw # WARNING: aquChr2 does not have seq # WARNING: aquChr2 does not have extFile # WARNING: aquChr2 does not have estOrientInfo # WARNING: aquChr2 does not have mrnaOrientInfo # copy it to hgwbeta scp -p aquChr2.pushQ.sql qateam@hgwbeta:/tmp ssh qateam@hgwbeta "./bin/x86_64/hgsql qapushq < /tmp/aquChr2.pushQ.sql" # in that pushQ entry walk through each entry and see if the # sizes will set properly ######################################################################### # BLATSERVERS ENTRY (DONE - 2017-05-09 - 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 ("aquChr2", "blat1c", "17866", "1", "0"); \ INSERT INTO blatServers (db, host, port, isTrans, canPcr) \ VALUES ("aquChr2", "blat1c", "17867", "0", "1");' \ hgcentraltest # test it with some sequence ############################################################################