# for emacs: -*- mode: sh; -*- # This file describes browser build for the orcOrc1 # Organism name: Orcinus orca (killer whale) # Must find the photograph first, can not continue until finding # the photograph. ######################################################################### # Initial steps, find photograph (DONE - 2016-05-31 - Hiram) # To start this initialBuild.txt document, from a previous assembly document: mkdir ~/kent/src/hg/makeDb/doc/orcOrc1 cd ~/kent/src/hg/makeDb/doc/orcOrc1 sed -e 's/rouAeg/orcOrc/g; s/RouAeg/OrcOrc/g; s/DONE/TBD/g;' \ ../rouAeg1/initialBuild.txt > initialBuild.txt # the files required are probably already here, take a look into: # /hive/data/outside/ncbi/genomes/refseq///all_assembly_versions # and merely symlink them in: mkdir -p /hive/data/genomes/orcOrc1/refseq cd -p /hive/data/genomes/orcOrc1/refseq ln -s /hive/data/outside/ncbi/genomes/refseq/vertebrate_mammalian/Orcinus_orca/all_assembly_versions/GCF_000331955.2_Oorc_1.1/* ./ # need to find the photo, check NCBI 'genome' page to see what photo they # display, if they do not have one, can usually find a public domain photo # in wikimedia commons: https://commons.wikimedia.org/wiki/Main_Page mkdir /hive/data/genomes/orcOrc1/photo cd /hive/data/genomes/orcOrc1/photo # this photo from: Oren Peles https://www.linkedin.com/in/oren-peles-398aa617 # to commons via: https://commons.wikimedia.org/wiki/User:MathKnight wget --timestamping \ https://upload.wikimedia.org/wikipedia/commons/3/37/Killerwhales_jumping.jpg jhead -ft Killerwhales_jumping.jpg convert -quality 80 -geometry 400x300 Killerwhales_jumping.jpg Orcinus_orca.jpg # check this Prcomis+prca.jpg into ~/kent/src/hg/htdocs/images/ # and copy that to /usr/local/apache/htdocs/images/ # construct the required photoReference.txt cd /hive/data/genomes/orcOrc1 printf "photoCreditURL http://www.afsc.noaa.gov/Quarterly/amj2005/divrptsNMML3.htm photoCreditName Robert Pitman (NOAA)\n" > photoReference.txt # this information is from the top of # refseq/*_assembly_report.txt # (aka: refseq/GCF_000331955.2_Oorc_1.1_assembly_report.txt) # Assembly name: Oorc_1.1 # Organism name: Orcinus orca (killer whale) # Isolate: Morgan # Sex: female # Taxid: 9733 # BioSample: SRS365047 # BioProject: PRJNA189949 # Submitter: Marine mammals # Date: 2013-1-31 # Assembly type: haploid # Release type: major # Assembly level: Scaffold # Genome representation: full # WGS project: ANOL02 # Assembly method: AllPaths v. 41070; ATLAS-link v. 1.0; ATLAS-gapfill v. 2.2 # Genome coverage: 200.0x # Sequencing technology: Illumina HiSeq # RefSeq category: Representative Genome # GenBank assembly accession: GCA_000331955.2 # RefSeq assembly accession: GCF_000331955.2 # RefSeq assembly and GenBank assemblies identical: yes # ## Assembly-Units: ## GenBank Unit Accession RefSeq Unit Accession Assembly-Unit name ## GCA_000331965.1 GCF_000331965.1 Primary Assembly ## GCA_000612095.1 GCF_000612095.1 non-nuclear ############################################################################# # establish config.ra file (DONE - Hiram - 2016-05-31) cd /hive/data/genomes/orcOrc1 ~/kent/src/hg/utils/automation/prepConfig.pl orcOrc1 mammal whale \ ./refseq/*_assembly_report.txt # verify it looks sane cat orcOrc1.config.ra # config parameters for makeGenomeDb.pl: db orcOrc1 clade mammal scientificName Orcinus orca commonName Killer whale assemblyDate Jan. 2013 assemblyLabel Marine mammals assemblyShortLabel Oorc_1.1 orderKey 11489 # mitochondrial sequence included in refseq release # mitoAcc NC_023889.1 mitoAcc none fastaFiles /hive/data/genomes/orcOrc1/ucsc/*.fa.gz agpFiles /hive/data/genomes/orcOrc1/ucsc/*.agp # qualFiles none dbDbSpeciesDir whale photoCreditURL http://www.afsc.noaa.gov/Quarterly/amj2005/divrptsNMML3.htm photoCreditName Robert Pitman (NOAA) ncbiGenomeId 14034 ncbiAssemblyId 556608 ncbiAssemblyName Oorc_1.1 ncbiBioProject 189949 ncbiBioSample SRS365047 genBankAccessionID GCF_000331955.2 taxId 9733 ############################################################################# # setup UCSC named files (DONE - 2016-05-31 - Hiram) mkdir /hive/data/genomes/orcOrc1/ucsc cd /hive/data/genomes/orcOrc1/ucsc # measure what is in the refseq release: faSize ../refseq/*genomic.fna.gz # 2372919875 bases (123337763 N's 2249582112 real 1513882205 upper # 735699907 lower) in 1668 sequences in 1 files # Total size: mean 1422613.8 sd 4344060.6 min 994 (NW_004439458.1) # max 41399143 (NW_004438415.1) median 3238 # %31.00 masked total, %32.70 masked real # check for duplicate sequences: time faToTwoBit -noMask ../refseq/*_genomic.fna.gz refseq.2bit # real 1m2.091s twoBitDup refseq.2bit # no output is a good result, otherwise, would have to eliminate duplicates # bash syntax here mitoAcc=`grep "^# mitoAcc" ../orcOrc1.config.ra | awk '{print $NF}'` printf "# mitoAcc %s\n" "$mitoAcc" # # mitoAcc NC_023889.1 zcat \ ../refseq/*_assembly_structure/non-nuclear/assem*/AGP/chrMT.comp.agp.gz \ | grep -v "^#" | sed -e "s/^$mitoAcc/chrM/;" > chrM.agp printf ">chrM\n" > chrM.fa twoBitToFa -noMask refseq.2bit:$mitoAcc stdout | grep -v "^>" >> chrM.fa # no longer need this 2bit rm refseq.2bit # the mito sequence is already named chrM printf "$mitoAcc\n" > excludeMito.txt # simple conversion of names .1 to v1 time faSomeRecords -exclude ../refseq/*_genomic.fna.gz excludeMito.txt \ stdout | sed -e 's/.1 Orc.*/v1/;' > ucsc.fa # real 2m13.627s cat chrM.fa >> ucsc.fa time gzip ucsc.fa # real 12m24.071s zcat ../refseq/*_assembly_structure/Primary_Assembly/unplaced_scaffolds/AGP/unplaced.scaf.agp.gz \ | sed -e 's/.1\t/v1\t/;' > ucsc.agp # verify correspondence faToTwoBit *.fa.gz test.2bit cat *.agp | checkAgpAndFa stdin test.2bit 2>&1 | tail # All AGP and FASTA entries agree - both files are valid # no longer need these 2bit files rm test.2bit refseq.2bit ############################################################################# # Initial database build (DONE - 2016-05-31 - Hiram) # verify sequence and AGP are OK: time (makeGenomeDb.pl -workhorse=hgwdev -dbHost=hgwdev -fileServer=hgwdev \ -stop=seq orcOrc1.config.ra) > seq.log 2>&1 time (makeGenomeDb.pl -workhorse=hgwdev -dbHost=hgwdev -fileServer=hgwdev \ -continue=agp -stop=agp orcOrc1.config.ra) > agp.log 2>&1 # then finish it off: time (makeGenomeDb.pl -workhorse=hgwdev -dbHost=hgwdev \ -fileServer=hgwdev -continue=db orcOrc1.config.ra) > db.log 2>&1 # real 20m39.022s # check in the trackDb files created and add to trackDb/makefile ############################################################################## # cpgIslands on UNMASKED sequence (DONE - 2016-05-31 - Hiram) mkdir /hive/data/genomes/orcOrc1/bed/cpgIslandsUnmasked cd /hive/data/genomes/orcOrc1/bed/cpgIslandsUnmasked time (doCpgIslands.pl -dbHost=hgwdev -bigClusterHub=ku -buildDir=`pwd` \ -tableName=cpgIslandExtUnmasked \ -maskedSeq=/hive/data/genomes/orcOrc1/orcOrc1.unmasked.2bit \ -workhorse=hgwdev -smallClusterHub=ku orcOrc1) > do.log 2>&1 # real 6m3.280s cat fb.orcOrc1.cpgIslandExtUnmasked.txt # 37760057 bases of 2249582125 (1.679%) in intersection ############################################################################# # cytoBandIdeo - (DONE - 2016-05-31 - Hiram) mkdir /hive/data/genomes/orcOrc1/bed/cytoBand cd /hive/data/genomes/orcOrc1/bed/cytoBand makeCytoBandIdeo.csh orcOrc1 ############################################################################# # ucscToINSDC table/track (DONE - 2016-05-31 - Hiram) # the sequence here is working for a 'refseq' assembly with a chrM # situation may be specific depending upon what is available in the assembly mkdir /hive/data/genomes/orcOrc1/bed/ucscToINSDC cd /hive/data/genomes/orcOrc1/bed/ucscToINSDC # find accession for chrM grep chrM ../../orcOrc1.agp # chrM 1 16386 1 O NC_023889.1 1 16386 + # use that accession here: ~/kent/src/hg/utils/automation/ucscToINSDC.sh \ ../../refseq/GCF_*structure/Primary_Assembly NC_023889.1 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 > insdc.refseq.txt | sed -e 's/na\b/notAvailable/;' | awk '{printf "%s\t%s\n", $2, $1}' \ # the sed \b means to match word awk '{printf "%s\t0\t%d\n", $1,$2}' ../../chrom.sizes \ | sort > name.coordinate.tab # the tr commands avoid the problem of trying to use the -t argument # to the join command which doesn't accept -t'\t' but instead has # to use the unseen/can not copy command ctrl-v i join insdc.refseq.txt insdcToUcsc.txt | tr '[ ]' '[\t]' | sort -k3 \ | join -2 3 name.coordinate.tab - | tr '[ ]' '[\t]' | cut -f1-3,5 \ > ucscToINSDC.bed # should be same line counts throughout: wc -l * # 2490 insdc.refseq.txt # 2490 insdcToUcsc.txt # 2490 name.coordinate.tab # 2490 ucscToINSDC.bed # 2490 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 orcOrc1 ucscToINSDC stdin ucscToINSDC.bed checkTableCoords orcOrc1 # should cover %100 entirely: featureBits -countGaps orcOrc1 ucscToINSDC # 2372919875 bases of 2372919875 (100.000%) in intersection join -1 2 <(sort -k2 ucscToINSDC.txt) insdc.refseq.txt | tr '[ ]' '[\t]' \ | sort -k2 | join -2 2 name.coordinate.tab - | tr '[ ]' '[\t]' \ | cut -f1-4 > ucscToRefSeq.bed cut -f1 ucscToRefSeq.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 \ | sed -e 's/INSDC/RefSeq/g;' > ucscToRefSeq.sql hgLoadSqlTab orcOrc1 ucscToRefSeq ./ucscToRefSeq.sql ucscToRefSeq.bed checkTableCoords orcOrc1 -table=ucscToRefSeq # should cover %100 all bases: featureBits -countGaps orcOrc1 ucscToRefSeq # 2372919875 bases of 2372919875 (100.000%) in intersection ######################################################################### # fixup search rule for assembly track/gold table (DONE - 2016-06-02 - Hiram) cd ~/kent/src/hg/makeDb/trackDb/whale/orcOrc1 # preview prefixes and suffixes: hgsql -N -e "select frag from gold;" orcOrc1 \ | sed -e 's/[0-9][0-9]*//;' | sort | uniq -c # 80099 ANOL.1 # 1 NC_.1 # implies a search rule of: '[ACLNO_]+[0-9]+(\.[0-9]+)?' # verify this rule will find them all or eliminate them all: hgsql -N -e "select frag from gold;" orcOrc1 | wc -l # 80100 hgsql -N -e "select frag from gold;" orcOrc1 \ | egrep -e '[ACLNO_]+[0-9]+(\.[0-9]+)?' | wc -l # 80100 hgsql -N -e "select frag from gold;" orcOrc1 \ | egrep -v -e '[ACLNO_]+[0-9]+(\.[0-9]+)?' | wc -l # 0 # hence, add to trackDb/rhesus/orcOrc1/trackDb.ra searchTable gold shortCircuit 1 termRegex [ACLNO_]+[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 - 2016-05-31 - Hiram) mkdir /hive/data/genomes/orcOrc1/bed/repeatMasker cd /hive/data/genomes/orcOrc1/bed/repeatMasker time (doRepeatMasker.pl -buildDir=`pwd` \ -bigClusterHub=ku -dbHost=hgwdev -workhorse=hgwdev \ -smallClusterHub=ku orcOrc1) > do.log 2>&1 # real 333m8.377s cat faSize.rmsk.txt # 2372919875 bases (123337763 N's 2249582112 real 1268122803 upper # 981459309 lower) in 1668 sequences in 1 files # Total size: mean 1422613.8 sd 4344060.6 min 994 (NW_004439458v1) # max 41399143 (NW_004438415v1) median 3238 # %41.36 masked total, %43.63 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 orcOrc1 rmsk # 990617945 bases of 2372919875 (41.747%) in intersection # real 0m52.033s # why is it different than the faSize above ? # because rmsk masks out some N's as well as bases, the faSize count above # separates out the N's from the bases, it doesn't show lower case N's # with high contig count assemblies, faster way to get the same result: time hgsql -N -e 'select genoName,genoStart,genoEnd from rmsk;' orcOrc1 \ | bedSingleCover.pl stdin | ave -col=4 stdin | grep "^total" # total 990617945.000000 # real 0m31.882s ########################################################################## # running simple repeat (DONE - 2016-05-31 - Hiram) mkdir /hive/data/genomes/orcOrc1/bed/simpleRepeat cd /hive/data/genomes/orcOrc1/bed/simpleRepeat time (doSimpleRepeat.pl -buildDir=`pwd` -bigClusterHub=ku \ -dbHost=hgwdev -workhorse=hgwdev -smallClusterHub=ku \ orcOrc1) > do.log 2>&1 # real 203m10.885s cat fb.simpleRepeat # 26818967 bases of 2249582125 (1.192%) in intersection # add to rmsk after it is done: cd /hive/data/genomes/orcOrc1 twoBitMask orcOrc1.rmsk.2bit \ -add bed/simpleRepeat/trfMask.bed orcOrc1.2bit # you can safely ignore the warning about fields >= 13 twoBitToFa orcOrc1.2bit stdout | faSize stdin > faSize.orcOrc1.2bit.txt cat faSize.orcOrc1.2bit.txt # 2372919875 bases (123337763 N's 2249582112 real 1267334294 upper # 982247818 lower) in 1668 sequences in 1 files # Total size: mean 1422613.8 sd 4344060.6 min 994 (NW_004439458v1) # max 41399143 (NW_004438415v1) median 3238 # %41.39 masked total, %43.66 masked real rm /gbdb/orcOrc1/orcOrc1.2bit ln -s `pwd`/orcOrc1.2bit /gbdb/orcOrc1/orcOrc1.2bit ######################################################################### # CREATE MICROSAT TRACK (DONE - 2016-06-01 - Hiram) ssh hgwdev mkdir /cluster/data/orcOrc1/bed/microsat cd /cluster/data/orcOrc1/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 orcOrc1 microsat microsat.bed # Read 39117 elements of size 4 from microsat.bed ########################################################################## ## WINDOWMASKER (DONE - 2016-06-01 - Hiram) mkdir /hive/data/genomes/orcOrc1/bed/windowMasker cd /hive/data/genomes/orcOrc1/bed/windowMasker time (doWindowMasker.pl -buildDir=`pwd` -workhorse=hgwdev \ -dbHost=hgwdev orcOrc1) > do.log 2>&1 # real 221m19.392s # Masking statistics cat faSize.orcOrc1.cleanWMSdust.txt # 2372919875 bases (123337763 N's 2249582112 real 1501851639 upper # 747730473 lower) in 1668 sequences in 1 files # Total size: mean 1422613.8 sd 4344060.6 min 994 (NW_004439458v1) # max 41399143 (NW_004438415v1) median 3238 # %31.51 masked total, %33.24 masked real cat fb.orcOrc1.rmsk.windowmaskerSdust.txt # 524787444 bases of 2372919875 (22.116%) in intersection ######################################################################### # run up idKeys files for ncbiRefSeq (DONE - 2016-06-01 - Hiram) mkdir /hive/data/genomes/orcOrc1/bed/idKeys cd /hive/data/genomes/orcOrc1/bed/idKeys time (doIdKeys.pl -buildDir=`pwd` orcOrc1) > do.log 2>&1 # real 4m49.109s cat orcOrc1.keySignature.txt # 85c3526e11108a706155e5b801d508d6 ########################################################################## # ncbiRefSeq - (DONE - 2016-06-01 - Hiram) mkdir /hive/data/genomes/orcOrc1/bed/ncbiRefSeq cd /hive/data/genomes/orcOrc1/bed/ncbiRefSeq time (~/kent/src/hg/utils/automation/doNcbiRefSeq.pl \ -buildDir=`pwd` -bigClusterHub=ku -dbHost=hgwdev \ -stop=download \ -fileServer=hgwdev -smallClusterHub=ku -workhorse=hgwdev \ refseq vertebrate_mammalian Orcinus_orca \ GCF_000331955.2_Oorc_1.1 orcOrc1) > download.log 2>&1 # real 7m3.558s time (~/kent/src/hg/utils/automation/doNcbiRefSeq.pl \ -buildDir=`pwd` -bigClusterHub=ku -dbHost=hgwdev \ -continue=process -stop=process \ -fileServer=hgwdev -smallClusterHub=ku -workhorse=hgwdev \ refseq vertebrate_mammalian Orcinus_orca \ GCF_000331955.2_Oorc_1.1 orcOrc1) > process.log 2>&1 # real 2m42.862s time (~/kent/src/hg/utils/automation/doNcbiRefSeq.pl \ -buildDir=`pwd` -bigClusterHub=ku -dbHost=hgwdev \ -continue=load -stop=load \ -fileServer=hgwdev -smallClusterHub=ku -workhorse=hgwdev \ refseq vertebrate_mammalian Orcinus_orca \ GCF_000331955.2_Oorc_1.1 orcOrc1) > load.log 2>&1 # real 0m17.767s featureBits -countGaps orcOrc1 ncbiRefSeq # 45687450 bases of 2372919875 (1.925%) in intersection ########################################################################## # cpgIslands - (DONE - 2016-06-01 - Hiram) mkdir /hive/data/genomes/orcOrc1/bed/cpgIslands cd /hive/data/genomes/orcOrc1/bed/cpgIslands time (doCpgIslands.pl -dbHost=hgwdev -bigClusterHub=ku \ -workhorse=hgwdev -smallClusterHub=ku orcOrc1) > do.log 2>&1 # real 5m33.326s cat fb.orcOrc1.cpgIslandExt.txt # 28442572 bases of 2249582125 (1.264%) in intersection ############################################################################## # genscan - (DONE - 2016-06-01 - Hiram) mkdir /hive/data/genomes/orcOrc1/bed/genscan cd /hive/data/genomes/orcOrc1/bed/genscan time (doGenscan.pl -buildDir=`pwd` -workhorse=hgwdev -dbHost=hgwdev \ -bigClusterHub=ku orcOrc1) > do.log 2>&1 # real 25m18.870s # one job broken, run with window of 2,000,000: ./lastRunGsBig.csh NW_004438481v1 000 gtf/000/NW_004438481v1.gtf pep/000/NW_004438481v1.pep subopt/000/NW_004438481v1.bed # real 12m47.728s time (doGenscan.pl -buildDir=`pwd` -workhorse=hgwdev -dbHost=hgwdev \ -continue=makeBed -bigClusterHub=ku orcOrc1) > makeBed.log 2>&1 # real 1m0.711s cat fb.orcOrc1.genscan.txt # 52075483 bases of 2249582125 (2.315%) in intersection cat fb.orcOrc1.genscanSubopt.txt # 49181696 bases of 2249582125 (2.186%) in intersection ######################################################################## # Create kluster run files (DONE - 2016-06-01 - Hiram) # numerator is orcOrc1 gapless bases "real" as reported by: featureBits -noRandom -noHap orcOrc1 gap # 123337750 bases of 2249582125 (5.483%) 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 \( 2249582125 / 2861349177 \) \* 1024 # ( 2249582125 / 2861349177 ) * 1024 = 805.065007 # ==> use -repMatch=800 according to size scaled down from 1024 for human. # and rounded down to nearest 50 cd /hive/data/genomes/orcOrc1 blat orcOrc1.2bit \ /dev/null /dev/null -tileSize=11 -makeOoc=jkStuff/orcOrc1.11.ooc \ -repMatch=800 # Wrote 28974 overused 11-mers to jkStuff/orcOrc1.11.ooc # there are no non-bridged gaps hgsql -e 'select count(*) from gap;' orcOrc1 # +----------+ # | count(*) | # +----------+ # | 78432 | # +----------+ hgsql -e 'select count(*) from gap where bridge="no";' orcOrc1 # +----------+ # | count(*) | # +----------+ # | 0 | # +----------+ # if there were non-bridged gaps, make up a nonBridged.lft file # check non-bridged gaps to see what the typical size is: # hgsql -N \ # -e 'select * from gap where bridge="no" order by size;' orcOrc1 \ # | sort -k7,7nr | ave -col=7 stdin # most non-bridged gaps have size = 100 # decide on a minimum gap for this break, use either 100 or 5000 will # generate 13387 liftOver rows, but if use 6000, only got 11703 rows. # so use 100 here to get more liftOver row. # gapToLift -verbose=2 -minGap=100 orcOrc1 jkStuff/nonBridged.lft \ # -bedFile=jkStuff/nonBridged.bed ######################################################################## # GENBANK AUTO UPDATE (DONE - 2016-06-02 - Hiram) ssh hgwdev cd $HOME/kent/src/hg/makeDb/genbank git pull # /cluster/data/genbank/data/organism.lst shows: # #organism mrnaCnt estCnt refSeqCnt # Orcinus orca 26 0 20 # Edit src/lib/gbGenome.c to add new species # edit etc/genbank.conf to add orcOrc1 just after balAcu1 # orcOrc1 (killer whale) orcOrc1.serverGenome = /hive/data/genomes/orcOrc1/orcOrc1.2bit orcOrc1.clusterGenome = /hive/data/genomes/orcOrc1/orcOrc1.2bit orcOrc1.ooc = /hive/data/genomes/orcOrc1/jkStuff/orcOrc1.11.ooc orcOrc1.lift = no orcOrc1.refseq.mrna.native.pslCDnaFilter = ${lowCover.refseq.mrna.native.pslCDnaFilter} orcOrc1.refseq.mrna.xeno.pslCDnaFilter = ${lowCover.refseq.mrna.xeno.pslCDnaFilter} orcOrc1.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter} orcOrc1.genbank.mrna.xeno.pslCDnaFilter = ${lowCover.genbank.mrna.xeno.pslCDnaFilter} orcOrc1.genbank.est.native.pslCDnaFilter = ${lowCover.genbank.est.native.pslCDnaFilter} orcOrc1.refseq.mrna.native.load = no orcOrc1.refseq.mrna.xeno.load = yes orcOrc1.genbank.mrna.xeno.load = no orcOrc1.genbank.est.native.load = no orcOrc1.genbank.mrna.native.load = no orcOrc1.genbank.mrna.native.loadDesc = no orcOrc1.downloadDir = orcOrc1 orcOrc1.perChromTables = no # refseq.mrna native and xeno are default yes # genbank.mrna and genbank.est native are default yes, the xeno is default no orcOrc1.genbank.est.native.load = no git commit -m "Added orcOrc - Orcinus orca (killer whale) refs #17425" etc/genbank.conf src/lib/gbGenome.c git push # update /cluster/data/genbank/: make etc-update make install-server screen # control this business with a screen since it takes a while cd /cluster/data/genbank time ./bin/gbAlignStep -initial orcOrc1 # logFile: var/build/logs/2016.06.01-11:32:53.orcOrc1.initalign.log # real 167m43.804s tail -2 var/build/logs/2016.06.01-11:32:53.orcOrc1.initalign.log # hgwdev 2016.06.01-14:18:58 orcOrc1.initalign: Succeeded: orcOrc1 # hgwdev 2016.06.01-14:20:36 orcOrc1.initalign: finish # To re-do, rm the dir first: # /cluster/data/genbank/work/initial.orcOrc1 # load database when finished ssh hgwdev cd /cluster/data/genbank time ./bin/gbDbLoadStep -drop -initialLoad orcOrc1 # logFile: var/dbload/hgwdev/logs/2016.06.02-10:36:16.orcOrc1.dbload.log # real 5m35.289s tail -1 var/dbload/hgwdev/logs/2016.06.02-10:36:16.orcOrc1.dbload.log # hgwdev 2016.06.02-10:41:51 orcOrc1.dbload: finish # enable daily alignment and update of hgwdev cd ~/kent/src/hg/makeDb/genbank git pull # add orcOrc1 to: # etc/align.dbs etc/hgwdev.dbs git add etc/align.dbs etc/hgwdev.dbs git commit -m "Added orcOrc1 - killer whale - Orcinus orca - refs #17425" etc/align.dbs etc/hgwdev.dbs git push make etc-update ############################################################################# # augustus gene track (DONE - 2016-06-01 - Hiram) mkdir /hive/data/genomes/orcOrc1/bed/augustus cd /hive/data/genomes/orcOrc1/bed/augustus time (doAugustus.pl -buildDir=`pwd` -bigClusterHub=ku \ -species=human -dbHost=hgwdev \ -workhorse=hgwdev orcOrc1) > do.log 2>&1 # real 153m58.477s cat fb.orcOrc1.augustusGene.txt # 47282944 bases of 2249582125 (2.102%) in intersection ######################################################################### # BLATSERVERS ENTRY (DONE - 2016-06-02 - 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 ("orcOrc1", "blat1a", "17862", "1", "0"); \ INSERT INTO blatServers (db, host, port, isTrans, canPcr) \ VALUES ("orcOrc1", "blat1a", "17863", "0", "1");' \ hgcentraltest # test it with some sequence ############################################################################ ## default position to casein beta (CSN2) gene (milk production) # (DONE - 2016-06-02 - Hiram) ssh hgwdev hgsql -e 'update dbDb set defaultPos="NW_004438441v1:339887-349875" where name="orcOrc1";' hgcentraltest ######################################################################### # all.joiner update, downloads and in pushQ - (TBD 2014-10-21 - Hiram) cd $HOME/kent/src/hg/makeDb/schema # fixup all.joiner until this is a clean output joinerCheck -database=orcOrc1 -tableCoverage all.joiner joinerCheck -database=orcOrc1 -times all.joiner joinerCheck -database=orcOrc1 -keys all.joiner cd /hive/data/genomes/orcOrc1 time (makeDownloads.pl orcOrc1) > downloads.log 2>&1 # real 15m52.648s # now ready for pushQ entry mkdir /hive/data/genomes/orcOrc1/pushQ cd /hive/data/genomes/orcOrc1/pushQ time (makePushQSql.pl -redmineList orcOrc1 > orcOrc1.pushQ.sql) 2> stderr.out # real 11m56.179s # check for errors in stderr.out, some are OK, e.g.: # WARNING: hgwdev does not have /gbdb/orcOrc1/wib/gc5Base.wib # WARNING: hgwdev does not have /gbdb/orcOrc1/wib/quality.wib # WARNING: hgwdev does not have /gbdb/orcOrc1/bbi/quality.bw # WARNING: orcOrc1 does not have seq # WARNING: orcOrc1 does not have extFile # copy it to hgwbeta scp -p orcOrc1.pushQ.sql qateam@hgwbeta:/tmp/ ssh qateam@hgwbeta "./bin/x86_64/hgsql qapushq < /tmp/orcOrc1.pushQ.sql" # in that pushQ entry walk through each entry and see if the # sizes will set properly ######################################################################### # lastz/chainNet swap mouse/mm10 (DONE - 2017-06-15 - Hiram) # alignment to mouse/mm10: cd /hive/data/genomes/mm10/bed/lastzOrcOrc1.2017-06-15 cat fb.mm10.chainOrcOrc1Link.txt # 832909116 bases of 2652783500 (31.398%) in intersection # and for the swap mkdir /hive/data/genomes/orcOrc1/bed/blastz.mm10.swap cd /hive/data/genomes/orcOrc1/bed/blastz.mm10.swap time (doBlastzChainNet.pl -verbose=2 \ /hive/data/genomes/mm10/bed/lastzOrcOrc1.2017-06-15/DEF \ -swap -syntenicNet \ -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \ -chainMinScore=3000 -chainLinearGap=medium) > swap.log 2>&1 # real 72m53.064s cat fb.orcOrc1.chainMm10Link.txt # 809350350 bases of 2249582125 (35.978%) in intersection time (doRecipBest.pl -workhorse=hgwdev orcOrc1 mm10 \ -buildDir=`pwd` -workhorse=hgwdev) > rbest.log 2>&1 # real 214m50.810s ############################################################################## # lastz/chainNet swap human/hg38 (DONE - 2016-06-03 - Hiram) # alignment to human/hg38: cd /hive/data/genomes/hg38/bed/lastzOrcOrc1.2016-06-03 cat fb.hg38.chainOrcOrc1Link.txt # 1544655174 bases of 3049335806 (50.655%) in intersection # and for the swap: mkdir /hive/data/genomes/orcOrc1/bed/blastz.hg38.swap cd /hive/data/genomes/orcOrc1/bed/blastz.hg38.swap time (doBlastzChainNet.pl -verbose=2 \ /hive/data/genomes/hg38/bed/lastzOrcOrc1.2016-06-03/DEF \ -swap -chainMinScore=3000 -chainLinearGap=medium \ -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \ -syntenicNet) > swap.log 2>&1 & # real 128m38.587s cat fb.orcOrc1.chainHg38Link.txt # 1447157896 bases of 2249582125 (64.330%) in intersection time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` orcOrc1 hg38) \ > rbest.log 2>&1 # real 467m24.661s #########################################################################