# for emacs: -*- mode: sh; -*- # This file describes browser build for the nanPar1 # Nanorana parkeri - Tibetan frog # http://www.ncbi.nlm.nih.gov/Traces/wgs/?val=JYOU01 # the description page is missing from the genbank directory # there is no chrMt sequence in this release or in NCBI nucleotide ############################################################################# # fetch sequence from new style download directory (DONE - 2015-03-03 - Hiram) # NCBI has redesigned their FTP download site, new type of address # and naming scheme mkdir -p /hive/data/genomes/nanPar1/genbank cd /hive/data/genomes/nanPar1/genbank time rsync -L -a -P \ rsync://ftp.ncbi.nlm.nih.gov/genomes/genbank/vertebrate_other/Nanorana_parkeri/all_assembly_versions/GCA_000935625.1_ASM93562v1/ ./ # sent 242 bytes received 1239116378 bytes 14492592.05 bytes/sec # total size is 1238963527 speedup is 1.00 # real 1m25.355s # measure what we have here: faSize GCA_000935625.1_ASM93562v1_genomic.fna.gz # 2053849526 bases (76078142 N's 1977771384 real 1221140057 # upper 756631327 lower) in 25187 sequences in 1 files # Total size: mean 81544.0 sd 330701.2 min 200 (JYOU01147511.1) # max 8606022 (KN905849.1) median 453 # %36.84 masked total, %38.26 masked real # that top-level file is the same as the unplaced scaffold file: faSize GCA_000935625.1_ASM93562v1_assembly_structure/Primary_Assembly/unplaced_scaffolds/FASTA/unplaced.scaf.fna.gz # 2053849526 bases (76078142 N's 1977771384 real 1977771384 upper 0 lower) # in 25187 sequences in 1 files # Total size: mean 81544.0 sd 330701.2 min 200 (JYOU01147511.1) # max 8606022 (KN905849.1) median 453 # %0.00 masked total, %0.00 masked real ############################################################################# # Assembly name: ASM93562v1 # Organism name: Nanorana parkeri (frogs & toads) # Isolate: BGI_ZX_2015 # Sex: female # Taxid: 125878 # BioSample: SAMN02720813 # BioProject: PRJNA344660 # Submitter: BGI-Shenzhen # Date: 2015-3-17 # Assembly type: haploid # Release type: major # Assembly level: Scaffold # Genome representation: full # WGS project: JYOU01 # Assembly method: SOAPdenovo v. 1.06 # Genome coverage: 83x # Sequencing technology: Illumina Genome Analyzer II # RefSeq category: Representative Genome # GenBank assembly accession: GCA_000935625.1 # RefSeq assembly accession: GCF_000935625.1 # RefSeq assembly and GenBank assemblies identical: no # ## Assembly-Units: ## GenBank Unit Accession RefSeq Unit Accession Assembly-Unit name ## GCA_000935635.1 GCF_000935635.1 Primary Assembly ## GCF_001746995.1 non-nuclear # ############################################################################# # fixup to UCSC naming scheme (DONE - 2015-03-19 - Hiram) mkdir /hive/data/genomes/nanPar1/ucsc cd /hive/data/genomes/nanPar1/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_000935625.1_ASM93562v1_assembly_structure/Primary_Assembly/unplaced_scaffolds/AGP/unplaced.scaf.agp.gz \ | grep -v "^#" | sed -e 's/\.1/v1/;' > chrUn.nanPar1.agp zcat ../genbank//GCA_000935625.1_ASM93562v1_assembly_structure/Primary_Assembly/unplaced_scaffolds/FASTA/unplaced.scaf.fna.gz \ | sed -e 's/.1 Nanorana .*/v1/;' > chrUn.nanPar1.fa # verify these two files are compatible: faToTwoBit chrUn.nanPar1.fa test.2bit checkAgpAndFa chrUn.nanPar1.agp test.2bit 2>&1 | tail # All AGP and FASTA entries agree - both files are valid rm test.2bit # fetch photo: mkdir /hive/data/genomes/nanPar1/photo cd /hive/data/genomes/nanPar1/photo wget --timestamping \ https://cns.utexas.edu/images/easyblog_shared/2015/nanorana-wang700.jpg convert -quality 80 -geometry "400x300" nanorana-wang700.jpg \ Nanorana_parkeri.jpg # check that into the source tree hg/htdocs/images/ git commit -m "photo courtesy Copyright (C) 2013 Kai Wang http://wangwenzhiwen.blog.163.com/ refs #14560" Nanorana_parkeri.jpg # and copy over to /usr/local/apache/htdocs/images/Nanorana_parkeri.jpg # permission obtained: # Subject: Re: photo usage request # From: Kai Wang # Date: Thu, 19 Mar 2015 15:06:52 -0700 # To: Hiram Clawson # Hi Hram # Sure. You are welcome to use the image at the website of U. Texas, and the reference URL looks good. # Best # Kai # 2015-3-19, # # 2:17, Hiram Clawson # # : # > Good Afternoon Kai Wang: # > I'd like to use your photo on the U.C. Santa Cruz genome browser as # > identification for this species Nanorana parkeri: # > # > http://calphotos.berkeley.edu/cgi/img_query?enlarge=0000+0000+0813+0727 # > http://calphotos.berkeley.edu/cgi/img_query?seq_num=578340&one=T # > # > I note it has been used at U. Texas: # > https://cns.utexas.edu/images/easyblog_shared/2015/nanorana-wang700.jpg # > # > We add credit notices and URL references to the photographer, note example: # > http://genome.ucsc.edu/cgi-bin/hgGateway?db=cavPor3 # > # > Would this be a good URL for your reference: http://wangwenzhiwen.blog.163.com/ # > # > --Hiram ############################################################################# # Initial database build (DONE - 2015-03-19 - Hiram) cd /hive/data/genomes/nanPar1 cat << '_EOF_' > nanPar1.config.ra # Config parameters for makeGenomeDb.pl: db nanPar1 clade vertebrate genomeCladePriority 50 scientificName Nanorana parkeri commonName Tibetan frog assemblyDate Mar. 2015 assemblyLabel ASM93562v1 assemblyShortLabel BGI_ZX_2015 orderKey 20312 mitoAcc none fastaFiles /hive/data/genomes/nanPar1/ucsc/*.fa agpFiles /hive/data/genomes/nanPar1/ucsc/*.agp # qualFiles none dbDbSpeciesDir frog photoCreditURL http://wangwenzhiwen.blog.163.com/ photoCreditName Copyright (C) 2013 Kai Wang ncbiGenomeId 36384 ncbiAssemblyId 302061 ncbiAssemblyName ASM93562v1 ncbiBioProject 243398 genBankAccessionID GCA_000935625.1 taxId 125878 '_EOF_' # << happy emacs # verify sequence and AGP are OK: time (makeGenomeDb.pl -workhorse=hgwdev -dbHost=hgwdev -fileServer=hgwdev \ -stop=agp nanPar1.config.ra) > agp.log 2>&1 # *** All done! (through the 'agp' step) # real 1m35.746s # then finish it off: time (makeGenomeDb.pl -workhorse=hgwdev -dbHost=hgwdev \ -fileServer=hgwdev -continue=db nanPar1.config.ra) > db.log 2>&1 # real 15m49.649s # check in the trackDb files created and add to trackDb/makefile ############################################################################## # cpgIslands on UNMASKED sequence (DONE - 2015-03-19 - Hiram) mkdir /hive/data/genomes/nanPar1/bed/cpgIslandsUnmasked cd /hive/data/genomes/nanPar1/bed/cpgIslandsUnmasked time (doCpgIslands.pl -dbHost=hgwdev -bigClusterHub=ku -buildDir=`pwd` \ -tableName=cpgIslandExtUnmasked \ -maskedSeq=/hive/data/genomes/nanPar1/nanPar1.unmasked.2bit \ -workhorse=hgwdev -smallClusterHub=ku nanPar1) > do.log 2>&1 # real 16m17.756s cat fb.nanPar1.cpgIslandExtUnmasked.txt # 80597444 bases of 1977771384 (4.075%) in intersection ############################################################################# # cytoBandIdeo - (DONE - 2015-03-19 - Hiram) mkdir /hive/data/genomes/nanPar1/bed/cytoBand cd /hive/data/genomes/nanPar1/bed/cytoBand makeCytoBandIdeo.csh nanPar1 ######################################################################### # 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 * # 25187 insdcToUcsc.txt # 25188 refseq.insdc.txt # 25187 ucsc.coordinate.tab # 25187 ucscToINSDC.bed # 25187 ucscToINSDC.txt # 25187 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 nanPar1 ucscToRefSeq ./ucscToRefSeq.sql ucscToRefSeq.bed # checkTableCoords should be silent checkTableCoords tupChi1 # each should cover %100 entirely: featureBits -countGaps nanPar1 ucscToINSDC # 2053849526 bases of 2053849526 (100.000%) in intersection featureBits -countGaps nanPar1 ucscToRefSeq # 2053849526 bases of 2053849526 (100.000%) in intersection ######################################################################### # ucscToINSDC table/track (DONE - 2015-03-20 - Hiram) mkdir /hive/data/genomes/nanPar1/bed/ucscToINSDC cd /hive/data/genomes/nanPar1/bed/ucscToINSDC ~/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 * # 25187 name.coordinate.tab # 25187 ucscToINSDC.bed # 25187 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 nanPar1 ucscToINSDC stdin ucscToINSDC.bed checkTableCoords nanPar1 # should cover %100 entirely: featureBits -countGaps nanPar1 ucscToINSDC # 2053849526 bases of 2053849526 (100.000%) in intersection ######################################################################### # add chromAlias table (DONE - 2017-03-13 - Hiram) mkdir /hive/data/genomes/nanPar1/bed/chromAlias cd /hive/data/genomes/nanPar1/bed/chromAlias hgsql -N -e 'select chrom,name,"refseq" from ucscToRefSeq;' nanPar1 \ > ucsc.refseq.tab hgsql -N -e 'select chrom,name,"genbank" from ucscToINSDC;' nanPar1 \ > ucsc.genbank.tab awk '{printf "%s\t%s\t%s\n", $2,$1,$3}' ucsc.genbank.tab ucsc.refseq.tab \ | sort > nanPar1.chromAlias.tab hgLoadSqlTab nanPar1 chromAlias ~/kent/src/hg/lib/chromAlias.sql \ nanPar1.chromAlias.tab ######################################################################### # fixup search rule for assembly track/gold table (DONE - 2015-03-20 - Hiram) hgsql -N -e "select frag from gold;" nanPar1 | sort | head -1 JYOU01000001.1 hgsql -N -e "select frag from gold;" nanPar1 | sort | tail -2 JYOU01147511.1 JYOU01147512.1 # verify this rule will find them all or eliminate them all: hgsql -N -e "select frag from gold;" nanPar1 | wc -l # 147512 hgsql -N -e "select frag from gold;" nanPar1 \ | egrep -e 'JYOU01[0-9]+(\.1)?' | wc -l # 147512 hgsql -N -e "select frag from gold;" nanPar1 \ | egrep -v -e 'JYOU01[0-9]+(\.1)?' | wc -l # 0 # hence, add to trackDb/tarsier/nanPar1/trackDb.ra searchTable gold shortCircuit 1 termRegex JYOU01[0-9]+(\.1)? query select chrom,chromStart,chromEnd,frag from %s where frag like '%s%%' searchPriority 8 ########################################################################## # running repeat masker (DONE - 2015-03-19 - Hiram) mkdir /hive/data/genomes/nanPar1/bed/repeatMasker cd /hive/data/genomes/nanPar1/bed/repeatMasker time (doRepeatMasker.pl -buildDir=`pwd` \ -bigClusterHub=ku -dbHost=hgwdev -workhorse=hgwdev \ -smallClusterHub=ku nanPar1) > do.log 2>&1 # real 232m59.124s cat faSize.rmsk.txt # 2053849526 bases (76078142 N's 1977771384 real 1950559334 upper # 27212050 lower) in 25187 sequences in 1 files # Total size: mean 81544.0 sd 330701.2 min 200 (JYOU01147511v1) # max 8606022 (KN905849v1) median 453 # %1.32 masked total, %1.38 masked real # most interesting, NCBI had %36.84 masked total, %38.26 masked real # I wonder how they did that ? 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 nanPar1 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 - 2015-03-19 - Hiram) mkdir /hive/data/genomes/nanPar1/bed/simpleRepeat cd /hive/data/genomes/nanPar1/bed/simpleRepeat time (doSimpleRepeat.pl -buildDir=`pwd` -bigClusterHub=ku \ -dbHost=hgwdev -workhorse=hgwdev -smallClusterHub=ku \ nanPar1) > do.log 2>&1 # real 20m20.609s cat fb.simpleRepeat # 112563839 bases of 1977771384 (5.691%) in intersection # using the Window Masker result: cd /hive/data/genomes/nanPar1 twoBitMask bed/windowMasker/nanPar1.cleanWMSdust.2bit \ -add bed/simpleRepeat/trfMask.bed nanPar1.2bit # you can safely ignore the warning about fields >= 13 twoBitToFa nanPar1.2bit stdout | faSize stdin > faSize.nanPar1.2bit.txt cat faSize.nanPar1.2bit.txt # 2053849526 bases (76078142 N's 1977771384 real 1208345365 # upper 769426019 lower) in 25187 sequences in 1 files # Total size: mean 81544.0 sd 330701.2 min 200 (JYOU01147511v1) # max 8606022 (KN905849v1) median 453 # %37.46 masked total, %38.90 masked real rm /gbdb/nanPar1/nanPar1.2bit ln -s `pwd`/nanPar1.2bit /gbdb/nanPar1/nanPar1.2bit ########################################################################## # CREATE MICROSAT TRACK (DONE - 2015-06-22 - Hiram) ssh hgwdev mkdir /cluster/data/nanPar1/bed/microsat cd /cluster/data/nanPar1/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 nanPar1 microsat microsat.bed # Read 8213 elements of size 4 from microsat.bed ########################################################################## ## WINDOWMASKER (DONE - 2015-03-20 - Hiram) mkdir /hive/data/genomes/nanPar1/bed/windowMasker cd /hive/data/genomes/nanPar1/bed/windowMasker time (doWindowMasker.pl -buildDir=`pwd` -workhorse=hgwdev \ -dbHost=hgwdev nanPar1) > do.log 2>&1 # real 153m54.144s # Masking statistics cat faSize.nanPar1.cleanWMSdust.txt # 2053849526 bases (76078142 N's 1977771384 real 1208849805 upper # 768921579 lower) in 25187 sequences in 1 files # Total size: mean 81544.0 sd 330701.2 min 200 (JYOU01147511v1) # max 8606022 (KN905849v1) median 453 # %37.44 masked total, %38.88 masked real cat fb.nanPar1.rmsk.windowmaskerSdust.txt # 23839116 bases of 2053849526 (1.161%) in intersection ########################################################################## # cpgIslands - (DONE - 2015-03-20 - Hiram) mkdir /hive/data/genomes/nanPar1/bed/cpgIslands cd /hive/data/genomes/nanPar1/bed/cpgIslands time (doCpgIslands.pl -dbHost=hgwdev -bigClusterHub=ku \ -workhorse=hgwdev -smallClusterHub=ku nanPar1) > do.log 2>&1 & # real 117m34.561s # failed during kluster hardMask operation, continuing: time (doCpgIslands.pl -dbHost=hgwdev -bigClusterHub=ku \ -continue=cpg -workhorse=hgwdev -smallClusterHub=ku nanPar1) \ > cpg.log 2>&1 & # real 10m28.915s cat fb.nanPar1.cpgIslandExt.txt # 13717904 bases of 1977771384 (0.694%) in intersection ######################################################################### # genscan - (DONE - 2015-03-20 - Hiram) mkdir /hive/data/genomes/nanPar1/bed/genscan cd /hive/data/genomes/nanPar1/bed/genscan time (doGenscan.pl -buildDir=`pwd` -workhorse=hgwdev -dbHost=hgwdev \ -bigClusterHub=ku nanPar1) > do.log 2>&1 # real 57m21.101s cat fb.nanPar1.genscan.txt # 55630505 bases of 1977771384 (2.813%) in intersection cat fb.nanPar1.genscanSubopt.txt # 58340692 bases of 1977771384 (2.950%) in intersection ######################################################################## # Create kluster run files (DONE - 2015-03-24 - Hiram) cd /hive/data/genomes/nanPar1 # numerator is nanPar1 gapless bases "real" as reported by: head -1 faSize.nanPar1.2bit.txt # 2053849526 bases (76078142 N's 1977771384 real 1208345365 upper # 76942601 lower) in 25187 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 \( 1977771384 / 2861349177 \) \* 1024 # ( 1977771384 / 2861349177 ) * 1024 = 707.791245 # ==> use -repMatch=700 according to size scaled down from 1024 for human. # and rounded down to nearest 50 cd /hive/data/genomes/nanPar1 time blat nanPar1.2bit \ /dev/null /dev/null -tileSize=11 -makeOoc=jkStuff/nanPar1.11.ooc \ -repMatch=700 # Wrote 23756 overused 11-mers to jkStuff/nanPar1.11.ooc # real 0m32.961s # 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;' nanPar1 # | 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 nanPar1 jkStuff/nanPar1.nonBridged.lft \ # -bedFile=jkStuff/nanPar1.nonBridged.bed # hgsql -N \ # -e 'select * from gap where bridge="no" order by size;' nanPar1 \ # | 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: 25187, total size: 2053849526, one half size: 1026924763 # cumulative N50 count contig contig size # 1026149130 545 KN906416v1 1073586 # 1026924763 one half size # 1027218231 546 KN906384v1 1069101 ############################################################################# # GENBANK AUTO UPDATE (DONE - 2015-06-09 - Hiram) ssh hgwdev cd $HOME/kent/src/hg/makeDb/genbank git pull # /cluster/data/genbank/data/organism.lst shows: # #organism mrnaCnt estCnt refSeqCnt # Nanorana parkeri 3 0 0 # Nanorana pleskei 3 0 0 # Nanorana yunnanensis 1 0 0 # edit etc/genbank.conf to add nanPar1 just before xenTro7 # nanPar1 (tibetan frog) nanPar1.serverGenome = /hive/data/genomes/nanPar1/nanPar1.2bit nanPar1.clusterGenome = /hive/data/genomes/nanPar1/nanPar1.2bit nanPar1.ooc = /hive/data/genomes/nanPar1/jkStuff/nanPar1.11.ooc nanPar1.lift = no nanPar1.perChromTables = no nanPar1.refseq.mrna.xeno.pslCDnaFilter = ${lowCover.refseq.mrna.xeno.pslCDnaFilter} nanPar1.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter} nanPar1.genbank.mrna.xeno.pslCDnaFilter = ${lowCover.genbank.mrna.xeno.pslCDnaFilter} nanPar1.genbank.est.native.pslCDnaFilter = ${lowCover.genbank.est.native.pslCDnaFilter} nanPar1.genbank.est.xeno.pslCDnaFilter = ${lowCover.genbank.est.xeno.pslCDnaFilter} nanPar1.downloadDir = nanPar1 nanPar1.refseq.mrna.native.load = no nanPar1.refseq.mrna.xeno.load = yes nanPar1.refseq.mrna.xeno.loadDesc = yes nanPar1.genbank.mrna.native.load = no nanPar1.genbank.mrna.native.loadDesc = no nanPar1.genbank.mrna.xeno.load = yes nanPar1.genbank.mrna.xeno.loadDesc = yes nanPar1.genbank.est.native.load = no nanPar1.genbank.est.native.loadDesc = no # nanPar1.upstreamGeneTbl = ensGene # Edit src/lib/gbGenome.c to add new species. git commit -m "Added nanPar Nanorana parkeri refs #15056" \ etc/genbank.conf src/lib/gbGenome.c git push # update /cluster/data/genbank/etc/: make etc-update # update /cluster/data/genbank/bin/: make install-server screen # control this business with a screen since it takes a while cd /cluster/data/genbank time ./bin/gbAlignStep -initial nanPar1 # logFile: var/build/logs/2015.05.27-15:45:35.nanPar1.initalign.log # real 1651m57.350s # To re-do, rm the dir first: # /cluster/data/genbank/work/initial.nanPar1 # load database when finished ssh hgwdev cd /cluster/data/genbank time ./bin/gbDbLoadStep -drop -initialLoad nanPar1 # logFile: var/dbload/hgwdev/logs/2015.06.09-14:34:12.nanPar1.dbload.log # real 128m32.009s # enable daily alignment and update of hgwdev cd ~/kent/src/hg/makeDb/genbank git pull # add nanPar1 to: # vi etc/align.dbs etc/hgwdev.dbs git commit -m "Added nanPar1 - Tibetan frog refs #15056" \ etc/align.dbs etc/hgwdev.dbs git push make etc-update ############################################################################ # BLATSERVERS ENTRY (DONE - 2017-03-22 - 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 ("nanPar1", "blat1b", "17874", "1", "0"); \ INSERT INTO blatServers (db, host, port, isTrans, canPcr) \ VALUES ("nanPar1", "blat1b", "17875", "0", "1");' \ hgcentraltest # test it with some sequence ############################################################################ ## reset default position to MAOA gene (Monoamine Oxidase A from monDom5) ## (DONE - 2017-03-22 - Hiram) ssh hgwdev hgsql -e 'update dbDb set defaultPos="KN906736v1:655217-696237" where name="nanPar1";' hgcentraltest ############################################################################ # all.joiner update, downloads and in pushQ - (DONE - 2015-06-22 - Hiram) cd $HOME/kent/src/hg/makeDb/schema # fixup all.joiner until this is a clean output joinerCheck -database=nanPar1 -tableCoverage all.joiner joinerCheck -database=nanPar1 -times all.joiner joinerCheck -database=nanPar1 -keys all.joiner cd /hive/data/genomes/nanPar1 time makeDownloads.pl nanPar1 > downloads.log 2>&1 # real 13m42.027s # now ready for pushQ entry mkdir /hive/data/genomes/nanPar1/pushQ cd /hive/data/genomes/nanPar1/pushQ makePushQSql.pl nanPar1 > nanPar1.pushQ.sql 2> stderr.out # check for errors in stderr.out, some are OK, e.g.: # WARNING: hgwdev does not have /gbdb/nanPar1/wib/gc5Base.wib # WARNING: hgwdev does not have /gbdb/nanPar1/wib/quality.wib # WARNING: hgwdev does not have /gbdb/nanPar1/bbi/qualityBw/quality.bw # WARNING: nanPar1 does not have seq # WARNING: nanPar1 does not have extFile # WARNING: nanPar1 does not have estOrientInfo # WARNING: nanPar1 does not have mrnaOrientInfo # copy it to hgwbeta scp -p nanPar1.pushQ.sql qateam@hgwbeta:/tmp ssh qateam@hgwbeta "./bin/x86_64/hgsql qapushq < /tmp/nanPar1.pushQ.sql" # in that pushQ entry walk through each entry and see if the # sizes will set properly #########################################################################