# for emacs: -*- mode: sh; -*- # This file describes the browser build for Onchocerca volvulus WS245 version ############################################################################## # download sequence, create UCSC sequence (DONE - 2015-06-24 - Hiram) # both the genbank and the WormBase releases are identical mkdir -p /hive/data/genomes/oncVol1/genbank cd /hive/data/genomes/oncVol1/genbank time rsync -L -a -P \ rsync://ftp.ncbi.nlm.nih.gov/genomes/genbank/invertebrate/Onchocerca_volvulus/all_assembly_versions/GCA_000499405.1_OVOC001/ ./ # sent 337 bytes received 95823961 bytes 8332547.65 bytes/sec # total size is 95810309 speedup is 1.00 # real 0m10.816s mkdir -p /hive/data/genomes/oncVol1/ws245 cd /hive/data/genomes/oncVol1/ws245 wget --no-parent --timestamping -m -nH --cut-dirs=6 \ ftp://ftp.sanger.ac.uk/pub/wormbase/releases/WS245/species/PRJEB513 mkdir /hive/data/genomes/oncVol1/ucsc cd /hive/data/genomes/oncVol1/ucsc zcat ../genbank/GCA_000499405.1_OVOC001_assembly_structure/Primary_Assembly/unplaced_scaffolds/FASTA/unplaced.scaf.fna.gz \ | sed -e 's/.1 Onchocerca.*/v1/;' | gzip -c > oncVol1.fa.gz zcat ../genbank/GCA_000499405.1_OVOC001_assembly_structure/Primary_Assembly/unplaced_scaffolds/AGP/unplaced.scaf.agp.gz | sed -e 's/\.1/v1/;' \ > oncVol1.agp # rerun this assembly, adding in the wolbachia sequence 2015-08-10 mkdir /hive/data/genomes/oncVol1/wolbachia rsync -L -a -P \ rsync://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000530755.1_W_O_volvulus_Cameroon_v3/ ./GCA_000530755.1/ zcat GCA_000530755.1/GCA_000530755.1_W_O_volvulus_Cameroon_v3_genomic.fna.gz | sed -e 's/^>.*/>wolbachia/;' | gzip -c > ../ucsc/wolbachia.fa.gz # find the accession from the gff.gz file: zcat */GCA_000530755.1_W_O_volvulus_Cameroon_v3_genomic.gff.gz # and the size faSize ../ucsc/wolbachia.fa.gz # use those values in this echo statement: echo -e 'wolbachia\t1\t960618\t1\tF\tHG810405.1\t1\t960618\t+' \ > ../ucsc/wolbachia.agp ############################################################################# # Initial database build (DONE - 2015-08-10 - Hiram) cd /hive/data/genomes/oncVol1 cat << '_EOF_' > oncVol1.config.ra # Config parameters for makeGenomeDb.pl: db oncVol1 clade worm genomeCladePriority 68 scientificName Onchocerca volvulus commonName O. volvulus assemblyDate Nov. 2013 assemblyLabel Wellcome Trust Sanger Institute O. volvulus genome project assemblyShortLabel WS241/O_volvulus_Cameroon_v3 orderKey 15000 mitoAcc AF015193.1 fastaFiles /hive/data/genomes/oncVol1/ucsc/*.fa.gz agpFiles /hive/data/genomes/oncVol1/ucsc/*.agp # qualFiles none dbDbSpeciesDir worm photoCreditURL http://parasite.org.au/blog/the-pugh-parasitology-collection/ photoCreditName R.E. Pugh parasitology collection ncbiGenomeId 2687 ncbiAssemblyId 81741 ncbiAssemblyName WS241/OVOC001 ncbiBioProject 226660 genBankAccessionID GCA_000499405.1 taxId 6282 '_EOF_' # << happy emacs # verify sequence and AGP are OK: time (makeGenomeDb.pl -workhorse=hgwdev -dbHost=hgwdev -fileServer=hgwdev \ -stop=agp oncVol1.config.ra) > agp.log 2>&1 # *** All done! (through the 'agp' step) # real 0m56.844s # then finish it off: time (makeGenomeDb.pl -workhorse=hgwdev -dbHost=hgwdev \ -fileServer=hgwdev -continue=db oncVol1.config.ra) > db.log 2>&1 # real 2m14.033s # check in the trackDb files created and add to trackDb/makefile ############################################################################## # cpgIslands on UNMASKED sequence (DONE - 2015-08-10 - Hiram) mkdir /hive/data/genomes/oncVol1/bed/cpgIslandsUnmasked cd /hive/data/genomes/oncVol1/bed/cpgIslandsUnmasked time (doCpgIslands.pl -dbHost=hgwdev -bigClusterHub=ku -buildDir=`pwd` \ -tableName=cpgIslandExtUnmasked \ -maskedSeq=/hive/data/genomes/oncVol1/oncVol1.unmasked.2bit \ -workhorse=hgwdev -smallClusterHub=ku oncVol1) > do.log 2>&1 # real 2m25.273s cat fb.oncVol1.cpgIslandExtUnmasked.txt # 36560 bases of 94327777 (0.039%) in intersection ############################################################################# # cytoBandIdeo - (DONE - 2015-08-10 - Hiram) mkdir /hive/data/genomes/oncVol1/bed/cytoBand cd /hive/data/genomes/oncVol1/bed/cytoBand makeCytoBandIdeo.csh oncVol1 ######################################################################### # ucscToINSDC table/track (DONE - 2015-08-10 - Hiram) mkdir /hive/data/genomes/oncVol1/bed/ucscToINSDC cd /hive/data/genomes/oncVol1/bed/ucscToINSDC # find the chrM accession: grep chrM ../../*.agp # chrM 1 13747 2 F AF015193.1 1 13747 + # use that as the second argument here: ~/kent/src/hg/utils/automation/ucscToINSDC.sh \ ../../genbank/GCA_*assembly_structure/Primary_Assembly AF015193.1 # add the wolbachia: echo -e 'wolbachia\tHG810405.1' >> ucscToINSDC.txt 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 * # 710 name.coordinate.tab # 710 ucscToINSDC.bed # 710 ucscToINSDC.txt cut -f1 ucscToINSDC.bed | awk '{print length($0)}' | sort -n | tail -1 # 10 # use the 10 in this sed sed -e "s/21/10/" $HOME/kent/src/hg/lib/ucscToINSDC.sql \ | hgLoadSqlTab oncVol1 ucscToINSDC stdin ucscToINSDC.bed checkTableCoords oncVol1 # should cover %100 entirely: featureBits -countGaps oncVol1 ucscToINSDC # 96441526 bases of 96441526 (100.000%) in intersection ######################################################################### # fixup search rule for assembly track/gold table (DONE - 2015-08-10 - Hiram) hgsql -N -e "select frag from gold;" oncVol1 | sort | head -3 AF015193.1 CBVM010000001.1 CBVM010000002.1 hgsql -N -e "select frag from gold;" oncVol1 | sort | tail -2 CBVM010001288.1 HG810405.1 # verify this rule will find them all or eliminate them all: hgsql -N -e "select frag from gold;" oncVol1 | wc -l # 1291 hgsql -N -e "select frag from gold;" oncVol1 \ | egrep -e '[ACH][BFG][V08][M1][0-9]*(\.1)?' \ | wc -l # 1291 hgsql -N -e "select frag from gold;" oncVol1 \ | egrep -v -e '[ACH][BFG][V08][M1][0-9]*(\.1)?' \ | wc -l # 0 # hence, add to trackDb/worm/oncVol1/trackDb.ra searchTable gold shortCircuit 1 termRegex [ACH][BFG][V08][M1][0-9]*(\.1)? query select chrom,chromStart,chromEnd,frag from %s where frag like '%s%%' searchPriority 8 ########################################################################## # running repeat masker (DONE - 2015-08-10 - Hiram) mkdir /hive/data/genomes/oncVol1/bed/repeatMasker cd /hive/data/genomes/oncVol1/bed/repeatMasker time (doRepeatMasker.pl -buildDir=`pwd` \ -bigClusterHub=ku -dbHost=hgwdev -workhorse=hgwdev \ -smallClusterHub=ku oncVol1) > do.log 2>&1 # real 35m20.023s cat faSize.rmsk.txt # 97402144 bases (3074367 N's 94327777 real 90636600 upper 3691177 lower) # in 710 sequences in 1 files # Total size: mean 137186.1 sd 1673613.5 min 523 (HG738843v1) # max 28345163 (HG738137v1) median 2222 # %3.79 masked total, %3.91 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 oncVol1 rmsk # 3691189 bases of 97402144 (3.790%) in intersection # real 0m0.838s ########################################################################## # running simple repeat (DONE - 2015-08-10 - Hiram) mkdir /hive/data/genomes/oncVol1/bed/simpleRepeat cd /hive/data/genomes/oncVol1/bed/simpleRepeat time (doSimpleRepeat.pl -buildDir=`pwd` -bigClusterHub=ku \ -dbHost=hgwdev -workhorse=hgwdev -smallClusterHub=ku \ oncVol1) > do.log 2>&1 # real 11m34.657s cat fb.simpleRepeat # 1742579 bases of 94327777 (1.847%) in intersection # using the Window Masker result as indicated below ########################################################################## # CREATE MICROSAT TRACK (DONE - 2015-07-09 - Hiram) ssh hgwdev mkdir /cluster/data/oncVol1/bed/microsat cd /cluster/data/oncVol1/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 oncVol1 microsat microsat.bed # Read 518 elements of size 4 from microsat.bed ########################################################################## ## WINDOWMASKER (DONE - 2015-08-10 - Hiram) mkdir /hive/data/genomes/oncVol1/bed/windowMasker cd /hive/data/genomes/oncVol1/bed/windowMasker time (doWindowMasker.pl -buildDir=`pwd` -workhorse=hgwdev \ -dbHost=hgwdev oncVol1) > do.log 2>&1 # real 4m44.395s # Masking statistics cat faSize.oncVol1.cleanWMSdust.txt # 97402144 bases (3074367 N's 94327777 real 59410953 upper 34916824 lower) # in 710 sequences in 1 files # Total size: mean 137186.1 sd 1673613.5 min 523 (HG738843v1) # max 28345163 (HG738137v1) median 2222 # %35.85 masked total, %37.02 masked real cat fb.oncVol1.rmsk.windowmaskerSdust.txt # 3208699 bases of 97402144 (3.294%) in intersection # using this Window Masker result for final masking:: cd /hive/data/genomes/oncVol1 # you can safely ignore the warning about fields >= 13 twoBitMask bed/windowMasker/oncVol1.cleanWMSdust.2bit \ -add bed/simpleRepeat/trfMask.bed oncVol1.2bit # measure the final masking: twoBitToFa oncVol1.2bit stdout | faSize stdin > faSize.oncVol1.2bit.txt cat faSize.oncVol1.2bit.txt # 97402144 bases (3074367 N's 94327777 real 59397958 upper 34929819 lower) # in 710 sequences in 1 files # Total size: mean 137186.1 sd 1673613.5 min 523 (HG738843v1) # max 28345163 (HG738137v1) median 2222 # %35.86 masked total, %37.03 masked real # and reset the symlink rm /gbdb/oncVol1/oncVol1.2bit ln -s /hive/data/genomes/oncVol1/oncVol1.2bit /gbdb/oncVol1/oncVol1.2bit ########################################################################## # cpgIslands - (DONE - 2015-08-10 - Hiram) mkdir /hive/data/genomes/oncVol1/bed/cpgIslands cd /hive/data/genomes/oncVol1/bed/cpgIslands time (doCpgIslands.pl -dbHost=hgwdev -bigClusterHub=ku \ -workhorse=hgwdev -smallClusterHub=ku oncVol1) > do.log 2>&1 & # real 1m49.769s cat fb.oncVol1.cpgIslandExt.txt # 29163 bases of 94327777 (0.031%) in intersection ######################################################################### # augustus - (DONE - 2015-08-10 - Hiram) mkdir /hive/data/genomes/oncVol1/bed/augustus cd /hive/data/genomes/oncVol1/bed/augustus # XXX this is not specifically correct, the species caenorhabditis # is not necessarily accurate here time (doAugustus.pl -buildDir=`pwd` -bigClusterHub=ku \ -species=caenorhabditis -dbHost=hgwdev \ -workhorse=hgwdev oncVol1) > do.log 2>&1 & # real 60m34.630s cat fb.oncVol1.augustusGene.txt # 5644798 bases of 94327777 (5.984%) in intersection ######################################################################### # genscan - (DONE - 2015-08-10 - Hiram) mkdir /hive/data/genomes/oncVol1/bed/genscan cd /hive/data/genomes/oncVol1/bed/genscan time (doGenscan.pl -buildDir=`pwd` -workhorse=hgwdev -dbHost=hgwdev \ -bigClusterHub=ku oncVol1) > do.log 2>&1 # real 15m30.688s cat fb.oncVol1.genscan.txt # 2807060 bases of 94327777 (2.976%) in intersection cat fb.oncVol1.genscanSubopt.txt # 2328851 bases of 94327777 (2.469%) in intersection ######################################################################## # Create kluster run files (TBD - 2015-07-08 - Hiram) cd /hive/data/genomes/oncVol1 # numerator is oncVol1 gapless bases "real" as reported by: head -1 faSize.oncVol1.2bit.txt # 94076581 bases (7759220 N's 86317361 real 53341517 upper 32975844 lower) # in 9780 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 \( 86317361 / 2861349177 \) \* 1024 # ( 86317361 / 2861349177 ) * 1024 = 30.890665 # ==> use -repMatch=100 since 30 or 50 masks too much cd /hive/data/genomes/oncVol1 time blat oncVol1.2bit \ /dev/null /dev/null -tileSize=11 -makeOoc=jkStuff/oncVol1.11.ooc \ -repMatch=100 # Wrote 8527 overused 11-mers to jkStuff/oncVol1.11.ooc # real 0m1.846s # there are a few non-bridged gaps # check non-bridged gaps to see what the typical size is: hgsql -N -e 'select * from gap where bridge="no" order by size;' oncVol1 \ | ave -tableOut -col=7 stdin # min Q1 median Q3 max mean N sum stddev # 78831 79056 79362 79503 79503 79162.5 4 316650 320.991 # note the minimum non-bridged gap size is 78,831 gapToLift -verbose=2 -minGap=50000 oncVol1 jkStuff/oncVol1.nonBridged.lft \ -bedFile=jkStuff/oncVol1.nonBridged.bed # survey sizes: n50.pl chrom.sizes # reading: chrom.sizes # contig count: 9780, total size: 94076581, one half size: 47038290 # cumulative N50 count contig contig size # 46960459 61 Bmal_v3_scaffold61 194773 # 47038290 one half size # 47151548 62 Bmal_v3_scaffold62 191089 ############################################################################# # GENBANK AUTO UPDATE (TBD - 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 # Pristionchus pacificus 97 37470 0 # edit etc/genbank.conf to add oncVol1 just before priPac1 # oncVol1 (P. pacificus) oncVol1.serverGenome = /hive/data/genomes/oncVol1/oncVol1.2bit oncVol1.clusterGenome = /hive/data/genomes/oncVol1/oncVol1.2bit oncVol1.ooc = /hive/data/genomes/oncVol1/jkStuff/oncVol1.11.ooc oncVol1.lift = /hive/data/genomes/oncVol1/jkStuff/oncVol1.nonBridged.lft oncVol1.refseq.mrna.native.pslCDnaFilter = ${ordered.refseq.mrna.native.pslCDnaFilter} oncVol1.refseq.mrna.xeno.pslCDnaFilter = ${ordered.refseq.mrna.xeno.pslCDnaFilter} oncVol1.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter} oncVol1.genbank.mrna.xeno.pslCDnaFilter = ${ordered.genbank.mrna.xeno.pslCDnaFilter} oncVol1.genbank.est.native.pslCDnaFilter = ${ordered.genbank.est.native.pslCDnaFilter} oncVol1.refseq.mrna.native.load = yes oncVol1.refseq.mrna.xeno.load = yes oncVol1.refseq.mrna.xeno.loadDesc = yes # DO NOT NEED genbank.mrna.xeno except for human, mouse oncVol1.genbank.mrna.xeno.load = no oncVol1.genbank.est.native.load = yes oncVol1.genbank.est.native.loadDesc = no oncVol1.downloadDir = oncVol1 oncVol1.perChromTables = no git commit -m "Added oncVol1 - P. pacificus refs #15209" etc/genbank.conf git push # update /cluster/data/genbank/etc/: make etc-update screen # control this business with a screen since it takes a while cd /cluster/data/genbank time ./bin/gbAlignStep -initial oncVol1 # logFile: var/build/logs/2015.07.02-11:39:01.oncVol1.initalign.log # real 91m20.362s # To re-do, rm the dir first: # /cluster/data/genbank/work/initial.oncVol1 # load database when finished ssh hgwdev cd /cluster/data/genbank time ./bin/gbDbLoadStep -drop -initialLoad oncVol1 # logFile: var/dbload/hgwdev/logs/2015.07.06-09:51:31.oncVol1.dbload.log # real 18m34.687s # enable daily alignment and update of hgwdev cd ~/kent/src/hg/makeDb/genbank git pull # add oncVol1 to: # vi etc/align.dbs etc/hgwdev.dbs git commit -m "Added oncVol1 - Pristionchus pacificus refs #15209" \ etc/align.dbs etc/hgwdev.dbs git push make etc-update ######################################################################### # all.joiner update, downloads and in pushQ - (TBD - 2015-06-22 - Hiram) cd $HOME/kent/src/hg/makeDb/schema # fixup all.joiner until this is a clean output joinerCheck -database=oncVol1 -tableCoverage all.joiner joinerCheck -database=oncVol1 -times all.joiner joinerCheck -database=oncVol1 -keys all.joiner cd /hive/data/genomes/oncVol1 time makeDownloads.pl oncVol1 > downloads.log 2>&1 # real 13m42.027s # now ready for pushQ entry mkdir /hive/data/genomes/oncVol1/pushQ cd /hive/data/genomes/oncVol1/pushQ makePushQSql.pl oncVol1 > oncVol1.pushQ.sql 2> stderr.out # check for errors in stderr.out, some are OK, e.g.: # WARNING: hgwdev does not have /gbdb/oncVol1/wib/gc5Base.wib # WARNING: hgwdev does not have /gbdb/oncVol1/wib/quality.wib # WARNING: hgwdev does not have /gbdb/oncVol1/bbi/qualityBw/quality.bw # WARNING: oncVol1 does not have seq # WARNING: oncVol1 does not have extFile # WARNING: oncVol1 does not have estOrientInfo # WARNING: oncVol1 does not have mrnaOrientInfo # copy it to hgwbeta scp -p oncVol1.pushQ.sql qateam@hgwbeta:/tmp ssh qateam@hgwbeta "./bin/x86_64/hgsql qapushq < /tmp/oncVol1.pushQ.sql" # in that pushQ entry walk through each entry and see if the # sizes will set properly #############################################################################