# for emacs: -*- mode: sh; -*- # This file describes browser build for the bisBis1 # Bison - Bison bison bison # Assembly Name: Bison_UMD1.0 # Organism name: Bison bison bison # Taxid: 43346 # Submitter: University of Maryland # Date: 2014-10-8 # BioSample: SAMN02947321 # Assembly type: haploid # Release type: major # Assembly level: Scaffold # Genome representation: full # GenBank Assembly Accession: GCA_000754665.1 (latest) # RefSeq Assembly Accession: GCF_000754665.1 (species-representative latest) # RefSeq Assembly and GenBank Assemblies Identical: no # ## Assembly-Units: ## GenBank Unit Accession RefSeq Unit Accession Assembly-Unit name ## GCA_000754675.1 GCF_000754675.1 Primary Assembly ## GCF_000079715.1 non-nuclear ############################################################################# # fetch sequence from new style download directory (DONE - 2015-03-04 - Hiram) mkdir -p /hive/data/genomes/bisBis1/genbank cd /hive/data/genomes/bisBis1/genbank time rsync -L -a -P \ rsync://ftp.ncbi.nlm.nih.gov/genomes/genbank/vertebrate_mammalian/Bison_bison/all_assembly_versions/GCA_000754665.1_Bison_UMD1.0/ ./ # sent 280 bytes received 2071454458 bytes 16772912.86 bytes/sec # total size is 2071199887 speedup is 1.00 # real 2m3.042s # 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_000754665.1_Bison_UMD1.0_genomic.fna.gz # 2953606000 bases (195767988 N's 2757838012 real 1619197667 upper # 1138640345 lower) in 450181 sequences in 1 files # Total size: mean 6560.9 sd 233789.4 min 200 (JPYT01449433.1) # max 43721425 (KN265167.1) median 428 # %38.55 masked total, %41.29 masked real # that top-level file is the same as the unplaced scaffold file: faSize GCA_000754665.1_Bison_UMD1.0_assembly_structure/Primary_Assembly/unplaced_scaffolds/FASTA/unplaced.scaf.fna.gz # 2953606000 bases (195767988 N's 2757838012 real 2757838012 upper # 0 lower) in 450181 sequences in 1 files # Total size: mean 6560.9 sd 233789.4 min 200 (JPYT01449433.1) # max 43721425 (KN265167.1) median 428 # %0.00 masked total, %0.00 masked real ############################################################################# # fixup to UCSC naming scheme (DONE - 2015-03-05 - Hiram) mkdir /hive/data/genomes/bisBis1/ucsc cd /hive/data/genomes/bisBis1/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_000754665.1_Bison_UMD1.0_assembly_structure/Primary_Assembly/unplaced_scaffolds/AGP/unplaced.scaf.agp.gz \ | grep -v "^#" | sed -e 's/\.1/v1/;' > chrUn.bisBis1.agp zcat ../genbank/GCA_000754665.1_Bison_UMD1.0_assembly_structure/Primary_Assembly/unplaced_scaffolds/FASTA/unplaced.scaf.fna.gz \ | sed -e 's/.1 Bison .*/v1/;' > chrUn.bisBis1.fa # verify these two files are compatible: faToTwoBit chrUn.bisBis1.fa test.2bit checkAgpAndFa chrUn.bisBis1.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/bisBis1 cat << '_EOF_' > bisBis1.config.ra # Config parameters for makeGenomeDb.pl: db bisBis1 clade mammal genomeCladePriority 31 scientificName Bison bison bison commonName Bison assemblyDate Oct. 2014 assemblyLabel U. Maryland assemblyShortLabel Bison_UMD1.0 orderKey 2315 # mitoAcc from the RefSeq assembly GCF_000754665.1 mitoAcc NC_012346.1 fastaFiles /hive/data/genomes/bisBis1/ucsc/*.fa agpFiles /hive/data/genomes/bisBis1/ucsc/*.agp # qualFiles none dbDbSpeciesDir bison photoCreditURL http://genetics.tamu.edu/faculty/lauren_dobson photoCreditName Lauren Dobson - Texas A and M University ncbiGenomeId 8907 ncbiAssemblyId 237421 ncbiAssemblyName Bison_UMD1.0 ncbiBioProject 266339 genBankAccessionID GCA_000754665.1 taxId 43346 '_EOF_' # << happy emacs # verify sequence and AGP are OK: # temporary set sciName to just 'Bison bison' to get through the chrM # identification time (makeGenomeDb.pl -workhorse=hgwdev -dbHost=hgwdev -fileServer=hgwdev \ -stop=agp bisBis1.config.ra) > agp.log 2>&1 # *** All done! (through the 'agp' step) # real 66m20.834s # reset sciName to 'Bison bison bison' # then finish it off: time (makeGenomeDb.pl -workhorse=hgwdev -dbHost=hgwdev \ -fileServer=hgwdev -continue=db bisBis1.config.ra) > db.log 2>&1 # real 35m25.469s # check in the trackDb files created and add to trackDb/makefile # and clean up: rm -fr TemporaryTrackDbCheckout/ ########################################################################## # running repeat masker (DONE - 2015-03-07 - Hiram) mkdir /hive/data/genomes/bisBis1/bed/repeatMasker cd /hive/data/genomes/bisBis1/bed/repeatMasker # RM did not recognize "Bison bison bison" time (doRepeatMasker.pl -buildDir=`pwd` \ -bigClusterHub=ku -dbHost=hgwdev -workhorse=hgwdev \ -species="Bison bison" \ -smallClusterHub=ku bisBis1) > do.log 2>&1 # real 169m48.984s # after cluster difficulties: time (doRepeatMasker.pl -buildDir=`pwd` \ -bigClusterHub=ku -dbHost=hgwdev -workhorse=hgwdev \ -continue=cat -species="Bison bison" \ -smallClusterHub=ku bisBis1) > cat.log 2>&1 # real 47m40.940s cat faSize.rmsk.txt # 2953622319 bases (195767988 N's 2757854331 real 1454950144 # upper 1302904187 lower) in 450182 sequences in 1 files # Total size: mean 6561.0 sd 233789.2 min 200 (JPYT01449433v1) # max 43721425 (KN265167v1) median 428 # %44.11 masked total, %47.24 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 bisBis1 rmsk # 1313271477 bases of 2953622319 (44.463%) in intersection # real 4m15.819s # 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 - 2015-03-07 - Hiram) mkdir /hive/data/genomes/bisBis1/bed/simpleRepeat cd /hive/data/genomes/bisBis1/bed/simpleRepeat time (doSimpleRepeat.pl -buildDir=`pwd` -bigClusterHub=ku \ -dbHost=hgwdev -workhorse=hgwdev -smallClusterHub=ku \ bisBis1) > do.log 2>&1 # real 346m50.550s cat fb.simpleRepeat # 32820797 bases of 2757854331 (1.190%) in intersection # using the Window Masker result: cd /hive/data/genomes/bisBis1 twoBitMask bed/repeatMasker/bisBis1.rmsk.2bit \ -add bed/simpleRepeat/trfMask.bed bisBis1.2bit # you can safely ignore the warning about fields >= 13 twoBitToFa bisBis1.2bit stdout | faSize stdin > faSize.bisBis1.2bit.txt cat faSize.bisBis1.2bit.txt # 2953622319 bases (195767988 N's 2757854331 real 1454240084 # upper 1303614247 lower) in 450182 sequences in 1 files # Total size: mean 6561.0 sd 233789.2 min 200 (JPYT01449433v1) # max 43721425 (KN265167v1) median 428 # %44.14 masked total, %47.27 masked real rm /gbdb/bisBis1/bisBis1.2bit ln -s `pwd`/bisBis1.2bit /gbdb/bisBis1/bisBis1.2bit ########################################################################## # CREATE MICROSAT TRACK (DONE - 2015-06-22 - Hiram) ssh hgwdev mkdir /cluster/data/bisBis1/bed/microsat cd /cluster/data/bisBis1/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 bisBis1 microsat microsat.bed # Read 18532 elements of size 4 from microsat.bed ########################################################################## ## WINDOWMASKER (DONE - 2015-03-09 - Hiram) mkdir /hive/data/genomes/bisBis1/bed/windowMasker cd /hive/data/genomes/bisBis1/bed/windowMasker time (doWindowMasker.pl -buildDir=`pwd` -workhorse=hgwdev \ -dbHost=hgwdev bisBis1) > do.log 2>&1 # real 1553m26.596s # Masking statistics cat faSize.bisBis1.cleanWMSdust.txt # 2953622319 bases (195767988 N's 2757854331 real 1605760353 upper # 1152093978 lower) in 450182 sequences in 1 files # Total size: mean 6561.0 sd 233789.2 min 200 (JPYT01449433v1) # max 43721425 (KN265167v1) median 428 # %39.01 masked total, %41.78 masked real cat fb.bisBis1.rmsk.windowmaskerSdust.txt # 885186161 bases of 2953622319 (29.970%) in intersection ########################################################################## # cpgIslands - (DONE - 2015-03-09 - Hiram) mkdir /hive/data/genomes/bisBis1/bed/cpgIslands cd /hive/data/genomes/bisBis1/bed/cpgIslands time (doCpgIslands.pl -dbHost=hgwdev -bigClusterHub=ku \ -workhorse=hgwdev -smallClusterHub=ku bisBis1) > do.log 2>&1 & # real 169m34.228s cat fb.bisBis1.cpgIslandExt.txt # 21291289 bases of 2757854331 (0.772%) in intersection ############################################################################## # cpgIslands on UNMASKED sequence (DONE - 2015-03-08 - Hiram) mkdir /hive/data/genomes/bisBis1/bed/cpgIslandsUnmasked cd /hive/data/genomes/bisBis1/bed/cpgIslandsUnmasked time (doCpgIslands.pl -dbHost=hgwdev -bigClusterHub=ku -buildDir=`pwd` \ -tableName=cpgIslandExtUnmasked \ -maskedSeq=/hive/data/genomes/bisBis1/bisBis1.unmasked.2bit \ -workhorse=hgwdev -smallClusterHub=ku bisBis1) > do.log 2>&1 # real 201m35.328s cat fb.bisBis1.cpgIslandExtUnmasked.txt # 38121515 bases of 2757854331 (1.382%) in intersection ############################################################################# # cytoBandIdeo - (DONE - 2015-03-09 - Hiram) mkdir /hive/data/genomes/bisBis1/bed/cytoBand cd /hive/data/genomes/bisBis1/bed/cytoBand makeCytoBandIdeo.csh bisBis1 ######################################################################### # augustus - (DONE - 2015-05-28 - Hiram) mkdir /hive/data/genomes/bisBis1/bed/augustus cd /hive/data/genomes/bisBis1/bed/augustus export db="bisBis1" export species="human" doAugustus.pl -buildDir=`pwd` -bigClusterHub=ku \ -species=$species -dbHost=hgwdev -utr -workhorse=hgwdev $db cat fb.bisBis1.augustusGene.txt # 46677083 bases of 2757854331 (1.693%) in intersection ######################################################################### # genscan - (DONE - 2015-03-09 - Hiram) mkdir /hive/data/genomes/bisBis1/bed/genscan cd /hive/data/genomes/bisBis1/bed/genscan time (doGenscan.pl -buildDir=`pwd` -workhorse=hgwdev -dbHost=hgwdev \ -bigClusterHub=ku bisBis1) > do.log 2>&1 & # real 162m42.398s # Completed: 450181 of 450182 jobs # Crashed: 1 jobs # CPU time in finished jobs: 76248s 1270.81m 21.18h 0.88d 0.002 y # IO & Wait Time: 1792734s 29878.89m 497.98h 20.75d 0.057 y # Average job time: 4s 0.07m 0.00h 0.00d # Longest finished job: 1047s 17.45m 0.29h 0.01d # Submission to last job: 5004s 83.40m 1.39h 0.06d # one failed job completed manually window size 2,000,000, continuing: time (doGenscan.pl -buildDir=`pwd` -workhorse=hgwdev -dbHost=hgwdev \ -continue=makeBed -bigClusterHub=ku bisBis1) > makeBed.log 2>&1 & # real 31m34.043s cat fb.bisBis1.genscan.txt # 54795491 bases of 2757854331 (1.987%) in intersection cat fb.bisBis1.genscanSubopt.txt # 55924017 bases of 2757854331 (2.028%) in intersection ######################################################################## # Create kluster run files (DONE - 2015-03-09 - Hiram) cd /hive/data/genomes/bisBis1 # numerator is bisBis1 gapless bases "real" as reported by: head -1 faSize.bisBis1.2bit.txt # 2953622319 bases (195767988 N's 2757854331 real 1454240084 upper # 1303614247 lower) in 450182 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 \( 2757854331 / 2861349177 \) \* 1024 # ( 2757854331 / 2861349177 ) * 1024 = 986.961975 # ==> use -repMatch=950 according to size scaled down from 1024 for human. # and rounded down to nearest 50 cd /hive/data/genomes/bisBis1 time blat bisBis1.2bit \ /dev/null /dev/null -tileSize=11 -makeOoc=jkStuff/bisBis1.11.ooc \ -repMatch=950 # Wrote 34610 overused 11-mers to jkStuff/bisBis1.11.ooc # real 1m32.452s # 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;' bisBis1 # | 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 bisBis1 jkStuff/bisBis1.nonBridged.lft \ # -bedFile=jkStuff/bisBis1.nonBridged.bed # hgsql -N \ # -e 'select * from gap where bridge="no" order by size;' bisBis1 \ # | 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: 450182, total size: 2953622319, one half size: # 1476811159 # cumulative N50 count contig contig size # 1476498935 124 KN264768v1 6889849 # 1476811159 one half size # 1483372189 125 KN264981v1 6873254 ############################################################################# # 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 # Bison bison 56 0 0 # Bison bonasus 17 0 0 # edit etc/genbank.conf to add bisBis1 just before bosTau2 # bisBis1 (Bison) 450182 contigs bisBis1.serverGenome = /hive/data/genomes/bisBis1/bisBis1.2bit bisBis1.clusterGenome = /hive/data/genomes/bisBis1/bisBis1.2bit bisBis1.ooc = /hive/data/genomes/bisBis1/jkStuff/bisBis1.11.ooc bisBis1.lift = no bisBis1.perChromTables = no bisBis1.refseq.mrna.xeno.pslCDnaFilter = ${lowCover.refseq.mrna.xeno.pslCDnaFilter} bisBis1.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter} bisBis1.genbank.mrna.xeno.pslCDnaFilter = ${lowCover.genbank.mrna.xeno.pslCDnaFilter} bisBis1.genbank.est.native.pslCDnaFilter = ${lowCover.genbank.est.native.pslCDnaFilter} bisBis1.genbank.est.xeno.pslCDnaFilter = ${lowCover.genbank.est.xeno.pslCDnaFilter} bisBis1.downloadDir = bisBis1 bisBis1.refseq.mrna.native.load = yes bisBis1.refseq.mrna.xeno.load = yes bisBis1.refseq.mrna.xeno.loadDesc = yes bisBis1.genbank.mrna.native.load = no bisBis1.genbank.mrna.native.loadDesc = no # DO NOT NEED genbank.mrna.xeno except for human, mouse bisBis1.genbank.mrna.xeno.load = no bisBis1.genbank.mrna.xeno.loadDesc = no bisBis1.genbank.est.native.load = no bisBis1.genbank.est.native.loadDesc = no # bisBis1.upstreamGeneTbl = ensGene git commit -m "Added bisBis1; refs #15388" 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 bisBis Bison bison bison 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 bisBis1 # logFile: var/build/logs/2015.05.27-15:26:55.bisBis1.initalign.log # real 81m6.372s # To re-do, rm the dir first: # /cluster/data/genbank/work/initial.bisBis1 # load database when finished ssh hgwdev cd /cluster/data/genbank time ./bin/gbDbLoadStep -drop -initialLoad bisBis1 # logFile: var/dbload/hgwdev/logs/2015.05.28-14:52:25.bisBis1.dbload.log # real 5m11.618s # enable daily alignment and update of hgwdev cd ~/kent/src/hg/makeDb/genbank git pull # add bisBis1 to: # vi etc/align.dbs etc/hgwdev.dbs git commit -m "Added bisBis1 - Bison bison bison refs #15388" \ etc/align.dbs etc/hgwdev.dbs git push make etc-update ######################################################################### # ucscToRefSeq table/track (DONE - 2017-03-14 - Hiram) mkdir /hive/data/genomes/bisBis1/bed/ucscToRefSeq cd /hive/data/genomes/bisBis1/bed/ucscToRefSeq # there are far fewer contigs in the refSeq assembly than the genbank # this one has a chrM grep chrM ../../bisBis1.agp # chrM 1 16319 1902 F NC_012346.1 1 16319 + # lookup NC_012346.1 at NCBI Entrez to find the INSDC name: EU177871.1 cut -f1 ../../chrom.sizes | grep -v chrM | sed -e 's/v1//;' \ | awk '{printf "%sv1\t%s.1\n", $1, $1}' | sort > ucscToINSDC.txt printf "chrM\tEU177871.1\n" >> ucscToINSDC.txt # run up idKeys on the refseq assembly, then join them: join refseqKeys/bisBis1RefSeq.idKeys.txt ../idKeys/bisBis1.idKeys.txt \ | awk '{printf "%s\t%s\n", $3,$2}' | sort > ucscToRefSeq.tab join ucsc.coordinate.tab ucscToRefSeq.tab \ | awk '{printf "%s\t%d\t%d\t%s\n", $1,$2,$3,$4}' | sort > ucscToRefSeq.bed # the existing ucscToINSDC track has an incorrect name for chrM, # reload it with the correct name awk '{printf "%s\t0\t%d\n", $1,$2}' ../../chrom.sizes \ | sort > ucsc.coordinate.tab join ucsc.coordinate.tab ucscToINSDC.txt | tr '[ ]' '[\t]' \ | sort > ucscToINSDC.bed # this UCSC assembly is missing the RefSeq chrM sequence: wc -l *.tab *.txt *.bed # 450182 ucsc.coordinate.tab # 128431 ucscToRefSeq.tab # 450182 insdcToUcsc.txt # 450182 ucscToINSDC.txt # 450182 ucscToINSDC.bed # 128431 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 bisBis1 ucscToRefSeq ./ucscToRefSeq.sql ucscToRefSeq.bed export chrSize=`cut -f1 ucscToINSDC.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;' > ucscToINSDC.sql hgLoadSqlTab bisBis1 ucscToINSDC ./ucscToINSDC.sql ucscToINSDC.bed # checkTableCoords should be silent checkTableCoords bisBis1 # each should cover %100 entirely: featureBits -countGaps bisBis1 ucscToINSDC # 2953622319 bases of 2953622319 (100.000%) in intersection # this one does not cover everything featureBits -countGaps bisBis1 ucscToRefSeq # 2828031685 bases of 2953622319 (95.748%) in intersection ######################################################################### # add chromAlias table (DONE - 2017-03-13 - Hiram) mkdir /hive/data/genomes/bisBis1/bed/chromAlias cd /hive/data/genomes/bisBis1/bed/chromAlias hgsql -N -e 'select chrom,name,"refseq" from ucscToRefSeq;' bisBis1 \ > ucsc.refseq.tab hgsql -N -e 'select chrom,name,"genbank" from ucscToINSDC;' bisBis1 \ > ucsc.genbank.tab awk '{printf "%s\t%s\t%s\n", $2,$1,$3}' ucsc.genbank.tab ucsc.refseq.tab \ | sort > bisBis1.chromAlias.tab hgLoadSqlTab bisBis1 chromAlias ~/kent/src/hg/lib/chromAlias.sql \ bisBis1.chromAlias.tab ######################################################################### # ucscToINSDC table/track (DONE - 2015-03-10 - Hiram) mkdir /hive/data/genomes/bisBis1/bed/ucscToINSDC cd /hive/data/genomes/bisBis1/bed/ucscToINSDC ~/kent/src/hg/utils/automation/ucscToINSDC.sh \ ../../genbank/GCA_*assembly_structure/Primary_Assembly NC_012346.1 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 * # 450182 name.coordinate.tab # 450182 ucscToINSDC.bed # 450182 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 bisBis1 ucscToINSDC stdin ucscToINSDC.bed checkTableCoords bisBis1 # should cover %100 entirely: featureBits -countGaps bisBis1 ucscToINSDC # 1192725744 bases of 1192725744 (100.000%) in intersection ######################################################################### # fixup search rule for assembly track/gold table (DONE - 2015-03-10 - Hiram) hgsql -N -e "select frag from gold;" bisBis1 | sort | head -1 JPYT01000001.1 hgsql -N -e "select frag from gold;" bisBis1 | sort | tail -2 JPYT01792165.1 NC_012346.1 # verify this rule will find them all or eliminate them all: hgsql -N -e "select frag from gold;" bisBis1 | wc -l # 792166 hgsql -N -e "select frag from gold;" bisBis1 \ | egrep -e '[JN][PC][Y_][T0][0-9]+(\.1)?' | wc -l # 792166 hgsql -N -e "select frag from gold;" bisBis1 \ | egrep -v -e '[JN][PC][Y_][T0][0-9]+(\.1)?' | wc -l # 0 # hence, add to trackDb/tarsier/bisBis1/trackDb.ra searchTable gold shortCircuit 1 termRegex [JN][PC][Y_][T0][0-9]+(\.1)? query select chrom,chromStart,chromEnd,frag from %s where frag like '%s%%' searchPriority 8 ############################################################################ # 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 ("bisBis1", "blat1b", "17876", "1", "0"); \ INSERT INTO blatServers (db, host, port, isTrans, canPcr) \ VALUES ("bisBis1", "blat1b", "17877", "0", "1");' \ hgcentraltest # test it with some sequence ############################################################################ ## reset default position to Bos taurus casein kinase 1 alpha 1 CSNK1A1 ## gene (a milk production gene) ## (DONE - 2017-03-22 - Hiram) ssh hgwdev hgsql -e 'update dbDb set defaultPos="KN265006v1:10821934-10865801" where name="bisBis1";' hgcentraltest ############################################################################ # all.joiner update, downloads and in pushQ - (DONE 2014-10-21 - Steve) cd $HOME/kent/src/hg/makeDb/schema # fixup all.joiner until this is a clean output git commit -m "Added bisBis1 - Bison bison bison refs #15388" \ all.joiner joinerCheck -database=bisBis1 -keys all.joiner joinerCheck -database=bisBis1 -tableCoverage all.joiner joinerCheck -database=bisBis1 -times all.joiner cd /hive/data/genomes/bisBis1 time makeDownloads.pl bisBis1 > downloads.log 2>&1 # real 25m16.304s # now ready for pushQ entry mkdir /hive/data/genomes/bisBis1/pushQ cd /hive/data/genomes/bisBis1/pushQ time makePushQSql.pl bisBis1 > bisBis1.pushQ.sql 2> stderr.out # real 5m16.163s # check for errors in stderr.out, some are OK, e.g.: # WARNING: hgwdev does not have /gbdb/bisBis1/wib/gc5Base.wib # WARNING: hgwdev does not have /gbdb/bisBis1/wib/quality.wib # WARNING: hgwdev does not have /gbdb/bisBis1/bbi/qualityBw/quality.bw # WARNING: bisBis1 does not have seq # WARNING: bisBis1 does not have extFile # WARNING: bisBis1 does not have estOrientInfo # copy it to hgwbeta scp -p bisBis1.pushQ.sql qateam@hgwbeta:/tmp ssh qateam@hgwbeta "./bin/x86_64/hgsql qapushq < /tmp/bisBis1.pushQ.sql" ssh hgwbeta cd /tmp hgsql qapushq < bisBis1.pushQ.sql # in that pushQ entry walk through each entry and see if the # sizes will set properly #########################################################################