# for emacs: -*- mode: sh; -*- # This file describes the browser build for # Ascaris suum/pig roundworm WS245 version ############################################################################## # download sequence, create UCSC sequence (DONE - 2015-06-24 - Hiram) mkdir -p /hive/data/genomes/ascSuu1/genbank cd /hive/data/genomes/ascSuu1/genbank # there are three assemblies at NCBI rsync -L -a -P \ rsync://ftp.ncbi.nlm.nih.gov/genomes/genbank/invertebrate/Ascaris_suum/all_assembly_versions/GCA_000298755.1_AscSuum_1.0/ . rsync -L -a -P \ rsync://ftp.ncbi.nlm.nih.gov/genomes/genbank/invertebrate/Ascaris_suum/all_assembly_versions/GCA_000331935.2_AS1.0/ ./ rsync -L -a -P \ rsync://ftp.ncbi.nlm.nih.gov/genomes/genbank/invertebrate/Ascaris_suum/all_assembly_versions/GCA_000187025.2_ASM18702v2/ ./ # there are two at WormBase: mkdir -p /hive/data/genomes/ascSuu1/ws245 cd /hive/data/genomes/ascSuu1/ws245 wget --no-parent --timestamping -m -nH --cut-dirs=6 \ ftp://ftp.sanger.ac.uk/pub/wormbase/releases/WS245/species/PRJNA62057 wget --no-parent --timestamping -m -nH --cut-dirs=6 \ ftp://ftp.sanger.ac.uk/pub/wormbase/releases/WS245/species/PRJNA80881 # The genbank/GCA_000298755.1_AscSuum_1.0_genomic.fna.gz and # WormBase PRJNA80881/a_suum.PRJNA80881.WS245.genomic.fa.gz # seem equivalent, the large scaffolds are identical sized, but # have different composition ? genbank is newer mkdir /hive/data/genomes/ascSuu1/ucsc cd /hive/data/genomes/ascSuu1/ucsc zcat ../genbank/GCA_000298755.1_AscSuum_1.0_assembly_structure/Primary_Assembly/unplaced_scaffolds/FASTA/unplaced.scaf.fna.gz \ | sed -e 's/.1 Ascaris .*/v1/;' | gzip -c > ascSuu1.fa.gz zcat ../genbank/GCA_000298755.1_AscSuum_1.0_assembly_structure/Primary_Assembly/unplaced_scaffolds/AGP/unplaced.scaf.agp.gz \ | sed -e 's/\.1/v1/;' > ascSuu1.agp # obtain photo, CDC public domain photo mkdir /hive/data/genomes/ascSuu1/photo cd /hive/data/genomes/ascSuu1/photo wget --timestamping \ http://www.cdc.gov/dpdx/images/ascariasis/Ascaris_female.jpg # this image is already 300x300 so it can go as is # check into source tree # src/hg/htdocs/images/Ascaris_suum.jpg # and copy to /usr/local/apache/htdocs/images/Ascaris_suum.jpg ############################################################################# # Initial database build (DONE - 2015-07-13 - Hiram) cd /hive/data/genomes/ascSuu1 cat << '_EOF_' > ascSuu1.config.ra # Config parameters for makeGenomeDb.pl: db ascSuu1 clade worm genomeCladePriority 68 scientificName Ascaris suum commonName Pig roundworm assemblyDate Sep. 2012 assemblyLabel Beijing Genomics Institute assemblyShortLabel WS229/AscSuum_1.0 orderKey 16320 mitoAcc X54253.1 fastaFiles /hive/data/genomes/ascSuu1/ucsc/ascSuu1.fa.gz agpFiles /hive/data/genomes/ascSuu1/ucsc/ascSuu1.agp # qualFiles none dbDbSpeciesDir worm photoCreditURL http://www.cdc.gov/parasites/ascariasis/ photoCreditName Centers for Disease Control and Prevention ncbiGenomeId 350 ncbiAssemblyId 426198 ncbiAssemblyName WS229/AscSuum_1.0 ncbiBioProject 80881 genBankAccessionID GCA_000298755.1 taxId 6253 '_EOF_' # << happy emacs # verify sequence and AGP are OK: time (makeGenomeDb.pl -workhorse=hgwdev -dbHost=hgwdev -fileServer=hgwdev \ -stop=agp ascSuu1.config.ra) > agp.log 2>&1 # *** All done! (through the 'agp' step) # real 0m34.666s # then finish it off: time (makeGenomeDb.pl -workhorse=hgwdev -dbHost=hgwdev \ -fileServer=hgwdev -continue=db ascSuu1.config.ra) > db.log 2>&1 # real 2m38.873s # check in the trackDb files created and add to trackDb/makefile ############################################################################## # cpgIslands on UNMASKED sequence (DONE - 2015-07-13 - Hiram) mkdir /hive/data/genomes/ascSuu1/bed/cpgIslandsUnmasked cd /hive/data/genomes/ascSuu1/bed/cpgIslandsUnmasked time (doCpgIslands.pl -dbHost=hgwdev -bigClusterHub=ku -buildDir=`pwd` \ -tableName=cpgIslandExtUnmasked \ -maskedSeq=/hive/data/genomes/ascSuu1/ascSuu1.unmasked.2bit \ -workhorse=hgwdev -smallClusterHub=ku ascSuu1) > do.log 2>&1 # real 9m16.354s cat fb.ascSuu1.cpgIslandExtUnmasked.txt # 3040279 bases of 262604320 (1.158%) in intersection ############################################################################# # cytoBandIdeo - (DONE - 2015-07-13 - Hiram) mkdir /hive/data/genomes/ascSuu1/bed/cytoBand cd /hive/data/genomes/ascSuu1/bed/cytoBand makeCytoBandIdeo.csh ascSuu1 ######################################################################### # ucscToINSDC table/track (DONE - 2015-07-13 - Hiram) mkdir /hive/data/genomes/ascSuu1/bed/ucscToINSDC cd /hive/data/genomes/ascSuu1/bed/ucscToINSDC # find the chrM accession: grep chrM ../../*.agp # chrM 1 14284 4 F X54253.1 1 14284 + # use that as the second argument here: ~/kent/src/hg/utils/automation/ucscToINSDC.sh \ ../../genbank/GCA_000298755.1_AscSuum_1.0_assembly_structure/Primary_Assembly X54253.1 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 * # 5765 name.coordinate.tab # 5765 ucscToINSDC.bed # 5765 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 ascSuu1 ucscToINSDC stdin ucscToINSDC.bed checkTableCoords ascSuu1 # should cover %100 entirely: featureBits -countGaps ascSuu1 ucscToINSDC # 269573965 bases of 269573965 (100.000%) in intersection ######################################################################### # fixup search rule for assembly track/gold table (DONE - 2015-07-13 - Hiram) hgsql -N -e "select frag from gold;" ascSuu1 | sort | head -3 AMPH01000001.1 AMPH01000002.1 AMPH01000003.1 hgsql -N -e "select frag from gold;" ascSuu1 | sort | tail -2 AMPH01030842.1 X54253.1 # verify this rule will find them all or eliminate them all: hgsql -N -e "select frag from gold;" ascSuu1 | wc -l # 30843 hgsql -N -e "select frag from gold;" ascSuu1 \ | egrep -e '(AMPH010|X54253)[0-9]*(\.1)?' | wc -l # 30843 hgsql -N -e "select frag from gold;" ascSuu1 \ | egrep -v -e '(AMPH010|X54253)[0-9]*(\.1)?' | wc -l # 0 # hence, add to trackDb/worm/ascSuu1/trackDb.ra searchTable gold shortCircuit 1 termRegex (AMPH010|X54253)[0-9]*(\.1)? query select chrom,chromStart,chromEnd,frag from %s where frag like '%s%%' searchPriority 8 ########################################################################## # running repeat masker (DONE - 2015-07-13 - Hiram) mkdir /hive/data/genomes/ascSuu1/bed/repeatMasker cd /hive/data/genomes/ascSuu1/bed/repeatMasker time (doRepeatMasker.pl -buildDir=`pwd` \ -bigClusterHub=ku -dbHost=hgwdev -workhorse=hgwdev \ -smallClusterHub=ku ascSuu1) > do.log 2>&1 # real 259m36.195s cat faSize.rmsk.txt # 269573965 bases (6969646 N's 262604319 real 258927735 upper # 3676584 lower) in 12989 sequences in 1 files # Total size: mean 20754.0 sd 115105.2 min 189 (AMPH01005591v1) # max 3795215 (JH878907v1) median 414 # %1.36 masked total, %1.40 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 ascSuu1 rmsk # 3678296 bases of 269573965 (1.364%) in intersection # real 0m5.089s ########################################################################## # running simple repeat (DONE - 2015-07-13 - Hiram) mkdir /hive/data/genomes/ascSuu1/bed/simpleRepeat cd /hive/data/genomes/ascSuu1/bed/simpleRepeat time (doSimpleRepeat.pl -buildDir=`pwd` -bigClusterHub=ku \ -dbHost=hgwdev -workhorse=hgwdev -smallClusterHub=ku \ ascSuu1) > do.log 2>&1 # real 7m23.268s cat fb.simpleRepeat # 5752869 bases of 262604320 (2.191%) in intersection # using the Window Masker result as indicated below ########################################################################## # CREATE MICROSAT TRACK (DONE - 2015-07-23 - Hiram) ssh hgwdev mkdir /cluster/data/ascSuu1/bed/microsat cd /cluster/data/ascSuu1/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 ascSuu1 microsat microsat.bed # Read 1148 elements of size 4 from microsat.bed ########################################################################## ## WINDOWMASKER (DONE - 2015-07-14 - Hiram) mkdir /hive/data/genomes/ascSuu1/bed/windowMasker cd /hive/data/genomes/ascSuu1/bed/windowMasker time (doWindowMasker.pl -buildDir=`pwd` -workhorse=hgwdev \ -dbHost=hgwdev ascSuu1) > do.log 2>&1 # real 12m49.610s # Masking statistics cat faSize.ascSuu1.cleanWMSdust.txt # 269573965 bases (6969646 N's 262604319 real 206235073 upper # 56369246 lower) in 12989 sequences in 1 files # Total size: mean 20754.0 sd 115105.2 min 189 (AMPH01005591v1) # max 3795215 (JH878907v1) median 414 # %20.91 masked total, %21.47 masked real cat fb.ascSuu1.rmsk.windowmaskerSdust.txt # 2973361 bases of 269573965 (1.103%) in intersection # using this Window Masker result for final masking:: cd /hive/data/genomes/ascSuu1 # you can safely ignore the warning about fields >= 13 twoBitMask bed/windowMasker/ascSuu1.cleanWMSdust.2bit \ -add bed/simpleRepeat/trfMask.bed ascSuu1.2bit # measure the final masking: twoBitToFa ascSuu1.2bit stdout | faSize stdin > faSize.ascSuu1.2bit.txt cat faSize.ascSuu1.2bit.txt # 269573965 bases (6969646 N's 262604319 real 206195917 upper # 56408402 lower) in 12989 sequences in 1 files # Total size: mean 20754.0 sd 115105.2 min 189 (AMPH01005591v1) # max 3795215 (JH878907v1) median 414 # %20.93 masked total, %21.48 masked real # and reset the symlink rm /gbdb/ascSuu1/ascSuu1.2bit ln -s /hive/data/genomes/ascSuu1/ascSuu1.2bit /gbdb/ascSuu1/ascSuu1.2bit ########################################################################## # cpgIslands - (DONE - 2015-07-15 - Hiram) mkdir /hive/data/genomes/ascSuu1/bed/cpgIslands cd /hive/data/genomes/ascSuu1/bed/cpgIslands time (doCpgIslands.pl -dbHost=hgwdev -bigClusterHub=ku \ -workhorse=hgwdev -smallClusterHub=ku ascSuu1) > do.log 2>&1 & # real 38m40.524s cat fb.ascSuu1.cpgIslandExt.txt # 2314905 bases of 262604320 (0.882%) in intersection ######################################################################### # augustus - (DONE - 2015-07-15 - Hiram) mkdir /hive/data/genomes/ascSuu1/bed/augustus cd /hive/data/genomes/ascSuu1/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 ascSuu1) > do.log 2>&1 & # real 74m28.022s cat fb.ascSuu1.augustusGene.txt # 17430033 bases of 262604320 (6.637%) in intersection ######################################################################### # genscan - (DONE - 2015-07-15 - Hiram) mkdir /hive/data/genomes/ascSuu1/bed/genscan cd /hive/data/genomes/ascSuu1/bed/genscan time (doGenscan.pl -buildDir=`pwd` -workhorse=hgwdev -dbHost=hgwdev \ -bigClusterHub=ku ascSuu1) > do.log 2>&1 # real 28m2.072s cat fb.ascSuu1.genscan.txt # 12245917 bases of 262604320 (4.663%) in intersection cat fb.ascSuu1.genscanSubopt.txt # 12237266 bases of 262604320 (4.660%) in intersection ######################################################################## # Create kluster run files (DONE - 2015-08-18 - Hiram) cd /hive/data/genomes/ascSuu1 # numerator is ascSuu1 gapless bases "real" as reported by: head -1 faSize.ascSuu1.2bit.txt # 269573965 bases (6969646 N's 262604319 real 206195917 upper 56408402 lower) # in 12989 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 \( 262604319 / 2861349177 \) \* 1024 # ( 262604319 / 2861349177 ) * 1024 = 93.979031 # ==> use -repMatch=100 cd /hive/data/genomes/ascSuu1 time blat ascSuu1.2bit \ /dev/null /dev/null -tileSize=11 -makeOoc=jkStuff/ascSuu1.11.ooc \ -repMatch=100 # Wrote 19578 overused 11-mers to jkStuff/ascSuu1.11.ooc # real 0m4.766s # there are NO 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;' ascSuu1 \ # | 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 ascSuu1 jkStuff/ascSuu1.nonBridged.lft \ # -bedFile=jkStuff/ascSuu1.nonBridged.bed # survey sizes: n50.pl chrom.sizes # reading: chrom.sizes # contig count: 12989, total size: 269573965, one half size: 134786982 # cumulative N50 count contig contig size # 134535441 174 JH879080v1 414787 # 134786982 one half size # 134948503 175 JH879081v1 413062 ############################################################################# # GENBANK AUTO UPDATE (DONE - 2015-08-19 - Hiram/Brian) ssh hgwdev cd $HOME/kent/src/hg/makeDb/genbank git pull # /cluster/data/genbank/data/organism.lst shows: # organism mrnaCnt estCnt refSeqCnt # Ascaris suum 74205 56617 0 # edit etc/genbank.conf to add ascSuu1 just before priPac3 # ascSuu1 (Pig roundworm/Ascaris suum) ascSuu1.serverGenome = /hive/data/genomes/ascSuu1/ascSuu1.2bit ascSuu1.clusterGenome = /hive/data/genomes/ascSuu1/ascSuu1.2bit ascSuu1.ooc = /hive/data/genomes/ascSuu1/jkStuff/ascSuu1.11.ooc ascSuu1.lift = no # the nematodes have small introns ascSuu1.maxIntron = 100000 ascSuu1.perChromTables = no ascSuu1.refseq.mrna.native.pslCDnaFilter = ${lowCover.refseq.mrna.native.pslCDnaFilter} ascSuu1.refseq.mrna.xeno.pslCDnaFilter = ${lowCover.refseq.mrna.xeno.pslCDnaFilter} ascSuu1.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter} ascSuu1.genbank.mrna.xeno.pslCDnaFilter = ${lowCover.genbank.mrna.xeno.pslCDnaFilter} ascSuu1.genbank.est.native.pslCDnaFilter = ${lowCover.genbank.est.native.pslCDnaFilter} # refseq.mrna native and xeno are default yes # genbank.mrna and genbank.est native are default yes, the xeno is default no ascSuu1.downloadDir = ascSuu1 # Edit src/lib/gbGenome.c to add new species. git commit -m "Added ascSuu1 - Pig roundworm/Ascaris suum refs #15209" etc/genbank.conf src/lib/gbGenome.c git push # update /cluster/data/genbank/etc/: make etc-update make install-server screen # control this business with a screen since it takes a while cd /cluster/data/genbank # had assistance from Brian on this as there were difficulties time ./bin/gbAlignStep -initial ascSuu1 # logFile: var/build/logs/2015.08.19-13:09:42.ascSuu1.initalign.log # about 142 minutes == 2h 22m # To re-do, rm these two sets first: # /cluster/data/genbank/work/initial.ascSuu1 # /cluster/data/genbank/data/aligned/*/ascSuu1 # load database when finished ssh hgwdev cd /cluster/data/genbank time ./bin/gbDbLoadStep -drop -initialLoad ascSuu1 # logFile: var/dbload/hgwdev/logs/2015.08.19-18:03:13.ascSuu1.dbload.log # about 42 minutes # enable daily alignment and update of hgwdev cd ~/kent/src/hg/makeDb/genbank git pull # add ascSuu1 to: # vi etc/align.dbs etc/hgwdev.dbs git commit -m "Added ascSuu1 - Ascaris suum/Pig roundworm 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=ascSuu1 -tableCoverage all.joiner joinerCheck -database=ascSuu1 -times all.joiner joinerCheck -database=ascSuu1 -keys all.joiner cd /hive/data/genomes/ascSuu1 time makeDownloads.pl ascSuu1 > downloads.log 2>&1 # real 13m42.027s # now ready for pushQ entry mkdir /hive/data/genomes/ascSuu1/pushQ cd /hive/data/genomes/ascSuu1/pushQ makePushQSql.pl ascSuu1 > ascSuu1.pushQ.sql 2> stderr.out # check for errors in stderr.out, some are OK, e.g.: # WARNING: hgwdev does not have /gbdb/ascSuu1/wib/gc5Base.wib # WARNING: hgwdev does not have /gbdb/ascSuu1/wib/quality.wib # WARNING: hgwdev does not have /gbdb/ascSuu1/bbi/qualityBw/quality.bw # WARNING: ascSuu1 does not have seq # WARNING: ascSuu1 does not have extFile # WARNING: ascSuu1 does not have estOrientInfo # WARNING: ascSuu1 does not have mrnaOrientInfo # copy it to hgwbeta scp -p ascSuu1.pushQ.sql qateam@hgwbeta:/tmp ssh qateam@hgwbeta "./bin/x86_64/hgsql qapushq < /tmp/ascSuu1.pushQ.sql" # in that pushQ entry walk through each entry and see if the # sizes will set properly #############################################################################