# for emacs: -*- mode: sh; -*- # This file describes the browser build # for Ancylostoma ceylanicum/hookworm WS245 version ############################################################################## # download sequence, create UCSC sequence (DONE - 2015-06-24 - Hiram) mkdir -p /hive/data/genomes/ancCey1/genbank cd /hive/data/genomes/ancCey1/genbank rsync -L -a -P \ rsync://ftp.ncbi.nlm.nih.gov/genomes/genbank/invertebrate/Ancylostoma_ceylanicum/all_assembly_versions/GCA_000688135.1_Acey_2013.11.30.genDNA/ ./ mkdir -p /hive/data/genomes/ancCey1/ws245 cd /hive/data/genomes/ancCey1/ws245 wget --no-parent --timestamping -m -nH --cut-dirs=6 \ ftp://ftp.sanger.ac.uk/pub/wormbase/releases/WS245/species/PRJNA231479 # The genbank and WS245 sequences are identical mkdir /hive/data/genomes/ancCey1/ucsc cd /hive/data/genomes/ancCey1/ucsc zcat ../genbank/GCA_000688135.1_Acey_2013.11.30.genDNA_genomic.fna.gz \ | sed -e 's/.1 Ancylostoma ceylanicum .*/v1/;' | gzip -c > ancCey1.fa.gz hgFakeAgp ancCey1.fa.gz ancCey1.agp # obtain photo, CDC public domain photo mkdir /hive/data/genomes/ancCey1/photo cd /hive/data/genomes/ancCey1/photo wget --timestamping \ http://www.cdc.gov/dpdx/images/hookworm/Hookworm_filariform_A.jpg # this image is slightly larger than 400x300, reduce to 400x300: convert -geometry "400x300" Hookworm_filariform_A.jpg \ Ancylostoma_ceylanicum.jpg # check into source tree # src/hg/htdocs/images/Ancylostoma_ceylanicum.jpg # and copy to /usr/local/apache/htdocs/images/Ancylostoma_ceylanicum.jpg ############################################################################# # Initial database build (DONE - 2015-07-15 - Hiram) cd /hive/data/genomes/ancCey1 cat << '_EOF_' > ancCey1.config.ra # Config parameters for makeGenomeDb.pl: db ancCey1 clade worm genomeCladePriority 86 scientificName Ancylostoma ceylanicum commonName Hookworm assemblyDate Mar. 2014 assemblyLabel Cornell University Ancylostoma ceylanicum genome project assemblyShortLabel WS243/Acey_2013.11.30.genDNA orderKey 8680 mitoAcc none fastaFiles /hive/data/genomes/ancCey1/ucsc/ancCey1.fa.gz agpFiles /hive/data/genomes/ancCey1/ucsc/ancCey1.agp # qualFiles none dbDbSpeciesDir worm photoCreditURL http://www.cdc.gov/dpdx/hookworm/ photoCreditName Centers for Disease Control and Prevention ncbiGenomeId 10936 ncbiAssemblyId 177101 ncbiAssemblyName WS243/Acey_2013.11.30.genDNA ncbiBioProject 231479 genBankAccessionID GCA_000688135.1 taxId 53326 '_EOF_' # << happy emacs # verify sequence and AGP are OK: time (makeGenomeDb.pl -workhorse=hgwdev -dbHost=hgwdev -fileServer=hgwdev \ -stop=agp ancCey1.config.ra) > agp.log 2>&1 # *** All done! (through the 'agp' step) # real 0m25.167s # then finish it off: time (makeGenomeDb.pl -workhorse=hgwdev -dbHost=hgwdev \ -fileServer=hgwdev -continue=db ancCey1.config.ra) > db.log 2>&1 # real 2m41.361s # check in the trackDb files created and add to trackDb/makefile ############################################################################## # cpgIslands on UNMASKED sequence (DONE - 2015-07-15 - Hiram) mkdir /hive/data/genomes/ancCey1/bed/cpgIslandsUnmasked cd /hive/data/genomes/ancCey1/bed/cpgIslandsUnmasked time (doCpgIslands.pl -dbHost=hgwdev -bigClusterHub=ku -buildDir=`pwd` \ -tableName=cpgIslandExtUnmasked \ -maskedSeq=/hive/data/genomes/ancCey1/ancCey1.unmasked.2bit \ -workhorse=hgwdev -smallClusterHub=ku ancCey1) > do.log 2>&1 # real 47m11.464s cat fb.ancCey1.cpgIslandExtUnmasked.txt # 29181817 bases of 300914990 (9.698%) in intersection ############################################################################# # cytoBandIdeo - (DONE - 2015-07-15 - Hiram) mkdir /hive/data/genomes/ancCey1/bed/cytoBand cd /hive/data/genomes/ancCey1/bed/cytoBand makeCytoBandIdeo.csh ancCey1 ######################################################################### # ucscToINSDC table/track (DONE - 2015-07-15 - Hiram) mkdir /hive/data/genomes/ancCey1/bed/ucscToINSDC cd /hive/data/genomes/ancCey1/bed/ucscToINSDC zcat ../../genbank/GCA_000688135.1_Acey_2013.11.30.genDNA_genomic.fna.gz \ | grep "^>" | sed -e 's/.1 Ancylostoma ceylanicum .*//; s/^>//;' \ | awk '{printf "%sv1\t%s.1\n", $1,$1}' | sort > 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 * # 1736 name.coordinate.tab # 1736 ucscToINSDC.bed # 1736 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 ancCey1 ucscToINSDC stdin ucscToINSDC.bed checkTableCoords ancCey1 # should cover %100 entirely: featureBits -countGaps ancCey1 ucscToINSDC # 313092710 bases of 313092710 (100.000%) in intersection ######################################################################### # fixup search rule for assembly track/gold table (DONE - 2015-07-15 - Hiram) hgsql -N -e "select frag from gold;" ancCey1 | sort | head -3 JARK01000001v1_1 JARK01000001v1_10 JARK01000001v1_11 hgsql -N -e "select frag from gold;" ancCey1 | sort | tail -2 JARK01001736v1_8 JARK01001736v1_9 # verify this rule will find them all or eliminate them all: hgsql -N -e "select frag from gold;" ancCey1 | wc -l # 20876 hgsql -N -e "select frag from gold;" ancCey1 \ | egrep -e 'JARK0100[0-9]*(\_1)?' | wc -l # 20876 hgsql -N -e "select frag from gold;" ancCey1 \ | egrep -v -e 'JARK0100[0-9]*(\_1)?' | wc -l # 0 # hence, add to trackDb/worm/ancCey1/trackDb.ra searchTable gold shortCircuit 1 termRegex JARK0100[0-9]*(\_1)? query select chrom,chromStart,chromEnd,frag from %s where frag like '%s%%' searchPriority 8 ########################################################################## # running repeat masker (DONE - 2015-07-15 - Hiram) mkdir /hive/data/genomes/ancCey1/bed/repeatMasker cd /hive/data/genomes/ancCey1/bed/repeatMasker time (doRepeatMasker.pl -buildDir=`pwd` \ -bigClusterHub=ku -dbHost=hgwdev -workhorse=hgwdev \ -smallClusterHub=ku ancCey1) > do.log 2>&1 # real 40m21.202s cat faSize.rmsk.txt # 313092710 bases (12191100 N's 300901610 real 296911527 upper # 3990083 lower) in 1736 sequences in 1 files # Total size: mean 180352.9 sd 424774.6 min 509 (JARK01001336v1) # max 4802298 (JARK01001337v1) median 43364 # %1.27 masked total, %1.33 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 ancCey1 rmsk # 3990156 bases of 313092710 (1.274%) in intersection # real 0m1.444s ########################################################################## # running simple repeat (DONE - 2015-07-15 - Hiram) mkdir /hive/data/genomes/ancCey1/bed/simpleRepeat cd /hive/data/genomes/ancCey1/bed/simpleRepeat time (doSimpleRepeat.pl -buildDir=`pwd` -bigClusterHub=ku \ -dbHost=hgwdev -workhorse=hgwdev -smallClusterHub=ku \ ancCey1) > do.log 2>&1 # real 2m50.443s cat fb.simpleRepeat # 7847572 bases of 300914990 (2.608%) in intersection # using the Window Masker result as indicated below ########################################################################## # CREATE MICROSAT TRACK (DONE - 2015-07-15 - Hiram) ssh hgwdev mkdir /cluster/data/ancCey1/bed/microsat cd /cluster/data/ancCey1/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 ancCey1 microsat microsat.bed # Read 2223 elements of size 4 from microsat.bed ########################################################################## ## WINDOWMASKER (DONE - 2015-07-15 - Hiram) mkdir /hive/data/genomes/ancCey1/bed/windowMasker cd /hive/data/genomes/ancCey1/bed/windowMasker time (doWindowMasker.pl -buildDir=`pwd` -workhorse=hgwdev \ -dbHost=hgwdev ancCey1) > do.log 2>&1 # real 13m42.365s # Masking statistics cat faSize.ancCey1.cleanWMSdust.txt # 313092710 bases (12191100 N's 300901610 real 234592544 upper # 66309066 lower) in 1736 sequences in 1 files # Total size: mean 180352.9 sd 424774.6 min 509 (JARK01001336v1) # max 4802298 (JARK01001337v1) median 43364 # %21.18 masked total, %22.04 masked real cat fb.ancCey1.rmsk.windowmaskerSdust.txt # 3401224 bases of 313092710 (1.086%) in intersection # using this Window Masker result for final masking:: cd /hive/data/genomes/ancCey1 # you can safely ignore the warning about fields >= 13 twoBitMask bed/windowMasker/ancCey1.cleanWMSdust.2bit \ -add bed/simpleRepeat/trfMask.bed ancCey1.2bit # measure the final masking: twoBitToFa ancCey1.2bit stdout | faSize stdin > faSize.ancCey1.2bit.txt cat faSize.ancCey1.2bit.txt # 313092710 bases (12191100 N's 300901610 real 234535031 upper # 66366579 lower) in 1736 sequences in 1 files # Total size: mean 180352.9 sd 424774.6 min 509 (JARK01001336v1) # max 4802298 (JARK01001337v1) median 43364 # %21.20 masked total, %22.06 masked real # and reset the symlink rm /gbdb/ancCey1/ancCey1.2bit ln -s /hive/data/genomes/ancCey1/ancCey1.2bit /gbdb/ancCey1/ancCey1.2bit ########################################################################## # cpgIslands - (DONE - 2015-07-15 - Hiram) mkdir /hive/data/genomes/ancCey1/bed/cpgIslands cd /hive/data/genomes/ancCey1/bed/cpgIslands time (doCpgIslands.pl -dbHost=hgwdev -bigClusterHub=ku \ -workhorse=hgwdev -smallClusterHub=ku ancCey1) > do.log 2>&1 & # real 2m55.776s cat fb.ancCey1.cpgIslandExt.txt # 10027791 bases of 300914990 (3.332%) in intersection ######################################################################### # augustus - (DONE - 2015-07-15 - Hiram) mkdir /hive/data/genomes/ancCey1/bed/augustus cd /hive/data/genomes/ancCey1/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 ancCey1) > do.log 2>&1 & # real 54m56.771s cat fb.ancCey1.augustusGene.txt # 33081827 bases of 300914990 (10.994%) in intersection ######################################################################### # genscan - (DONE - 2015-07-15 - Hiram) mkdir /hive/data/genomes/ancCey1/bed/genscan cd /hive/data/genomes/ancCey1/bed/genscan time (doGenscan.pl -buildDir=`pwd` -workhorse=hgwdev -dbHost=hgwdev \ -bigClusterHub=ku ancCey1) > do.log 2>&1 # real 5m10.885s cat fb.ancCey1.genscan.txt # 18315189 bases of 300914990 (6.086%) in intersection cat fb.ancCey1.genscanSubopt.txt # 15435033 bases of 300914990 (5.129%) in intersection ######################################################################## # Create kluster run files (TBD - 2015-07-08 - Hiram) cd /hive/data/genomes/ancCey1 # numerator is ancCey1 gapless bases "real" as reported by: head -1 faSize.ancCey1.2bit.txt # 313092710 bases (12191100 N's 300901610 real 234535031 upper 66366579 lower) # in 1736 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 \( 300901610 / 2861349177 \) \* 1024 # ( 300901610 / 2861349177 ) * 1024 = 107.684602 # ==> use -repMatch=150 since 100 makes quite a few (Wrote 13661 overused) cd /hive/data/genomes/ancCey1 time blat ancCey1.2bit /dev/null /dev/null -tileSize=11 \ -makeOoc=jkStuff/ancCey1.11.ooc -repMatch=150 # Wrote 4676 overused 11-mers to jkStuff/ancCey1.11.ooc # real 0m4.930s # 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;' ancCey1 \ # | 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 ancCey1 jkStuff/ancCey1.nonBridged.lft \ # -bedFile=jkStuff/ancCey1.nonBridged.bed # survey sizes: n50.pl chrom.sizes # reading: chrom.sizes # contig count: 1736, total size: 313092710, one half size: 156546355 # cumulative N50 count contig contig size # 156517762 107 JARK01001443v1 669185 # 156546355 one half size # 157186174 108 JARK01001444v1 668412 ############################################################################# # GENBANK AUTO UPDATE (DONE - 2015-08-26 - Hiram) ssh hgwdev cd $HOME/kent/src/hg/makeDb/genbank git pull # /cluster/data/genbank/data/organism.lst shows: # #organism mrnaCnt estCnt refSeqCnt # Ancylostoma ceylanicum 40 10651 0 # edit etc/genbank.conf to add ancCey1 just before priPac3 # ancCey1 (A. ceylanicum) ancCey1.serverGenome = /hive/data/genomes/ancCey1/ancCey1.2bit ancCey1.clusterGenome = /hive/data/genomes/ancCey1/ancCey1.2bit ancCey1.ooc = /hive/data/genomes/ancCey1/jkStuff/ancCey1.11.ooc ancCey1.lift = no # the nematodes have small introns ancCey1.maxIntron = 10 ancCey1.perChromTables = no ancCey1.refseq.mrna.native.pslCDnaFilter = ${lowCover.refseq.mrna.native.pslCDnaFilter} ancCey1.refseq.mrna.xeno.pslCDnaFilter = ${lowCover.refseq.mrna.xeno.pslCDnaFilter} ancCey1.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter} ancCey1.genbank.mrna.xeno.pslCDnaFilter = ${lowCover.genbank.mrna.xeno.pslCDnaFilter} ancCey1.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 ancCey1.downloadDir = ancCey1 git commit -m "Added ancCey1 - A. ceylanicum refs #15209" etc/genbank.conf git push # update /cluster/data/genbank/etc/: make etc-update # adding ancCeyNames to src/lib/gbGenome.c git pull git commit -m "Added ancCeyNames - A. ceylanicum refs #15209" \ 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 ancCey1 # logFile: var/build/logs/2015.08.26-14:37:55.ancCey1.initalign.log # real 91m20.362s # To re-do, rm the dir first: # /cluster/data/genbank/work/initial.ancCey1 # to avoid failed load: cd /cluster/data/genbank/data/aligned/refseq.71/ancCey1 # find file with illegal name: grep AC_ */*xeno* # daily.2015.0725/mrna.xeno.alidx:AC_000192 1 0 # remove that line from that file # load database when finished ssh hgwdev cd /cluster/data/genbank time ./bin/gbDbLoadStep -drop -initialLoad ancCey1 # logFile: var/dbload/hgwdev/logs/2015.09.08-10:45:06.ancCey1.dbload.log # real 17m10.671s # enable daily alignment and update of hgwdev cd ~/kent/src/hg/makeDb/genbank git pull # add ancCey1 to: # vi etc/align.dbs etc/hgwdev.dbs git commit -m "Added ancCey1 - Ancylostoma ceylanicum 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=ancCey1 -tableCoverage all.joiner joinerCheck -database=ancCey1 -times all.joiner joinerCheck -database=ancCey1 -keys all.joiner cd /hive/data/genomes/ancCey1 time makeDownloads.pl ancCey1 > downloads.log 2>&1 # real 13m42.027s # now ready for pushQ entry mkdir /hive/data/genomes/ancCey1/pushQ cd /hive/data/genomes/ancCey1/pushQ makePushQSql.pl ancCey1 > ancCey1.pushQ.sql 2> stderr.out # check for errors in stderr.out, some are OK, e.g.: # WARNING: hgwdev does not have /gbdb/ancCey1/wib/gc5Base.wib # WARNING: hgwdev does not have /gbdb/ancCey1/wib/quality.wib # WARNING: hgwdev does not have /gbdb/ancCey1/bbi/qualityBw/quality.bw # WARNING: ancCey1 does not have seq # WARNING: ancCey1 does not have extFile # WARNING: ancCey1 does not have estOrientInfo # WARNING: ancCey1 does not have mrnaOrientInfo # copy it to hgwbeta scp -p ancCey1.pushQ.sql qateam@hgwbeta:/tmp ssh qateam@hgwbeta "./bin/x86_64/hgsql qapushq < /tmp/ancCey1.pushQ.sql" # in that pushQ entry walk through each entry and see if the # sizes will set properly #############################################################################