# for emacs: -*- mode: sh; -*- # This file describes how the browser for C. angaria WS245 version is built ############################################################################## # download sequence, create UCSC sequence (DONE - 2015-06-24 - Hiram) mkdir -p /hive/data/genomes/panRed1/genbank cd /hive/data/genomes/panRed1/genbank time rsync -L -a -P \ rsync://ftp.ncbi.nlm.nih.gov/genomes/genbank/invertebrate/Panagrellus_redivivus/all_assembly_versions/GCA_000341325.1_Pred3/ ./ mkdir -p /hive/data/genomes/panRed1/ws245 cd /hive/data/genomes/panRed1/ws245 wget --no-parent --timestamping -m -nH --cut-dirs=6 \ ftp://ftp.sanger.ac.uk/pub/wormbase/releases/WS245/species/PRJNA186477 mkdir /hive/data/genomes/panRed1/ucsc cd /hive/data/genomes/panRed1/ucsc # WormBase contig names are of the pattern: # >KB455460 1 2280433 # >KB455532 1 1000036 # >KB455127 1 861165 # >KB455382 1 814844 # >KB455536 1 783189 # ... # the genbank and ws245 names are identical except the ws245 is # missing the .1 on each name. Using the ws245 names to be compatible # with WormBase # no conversion of names to maintain equivalence with WormBase: zcat ../ws245/PRJNA186477/p_redivivus.PRJNA186477.WS245.genomic.fa.gz \ | sed -e 's/ .*//;' | gzip -c > panRed1.fa.gz hgFakeAgp panRed1.fa.gz panRed1.agp # correct photo from WikiMedia Commons: mkdir /hive/data/genomes/panRed1/photo cd /hive/data/genomes/panRed1/photo wget --timestamping \ https://upload.wikimedia.org/wikipedia/en/c/cf/Panagrellus_redivivus_Otago_University_Cold_Stage.jpg convert -quality 80 -geometry 400x300 Panagrellus_redivivus_Otago_University_Cold_Stage.jpg \ Panagrellus_redivivus.jpg identify Panagrellus_redivivus.jpg # Panagrellus_redivivus.jpg JPEG 400x300 400x300+0+0 # reference: http://www.otago.ac.nz/zoology/staff/otago008939.html # WikiMedia Commons David Wharton, University of Otago # https://en.wikipedia.org/wiki/File:Panagrellus_redivivus_Otago_University_Cold_Stage.jpg ############################################################################# # Initial database build (DONE - 2015-07-01 - Hiram) cd /hive/data/genomes/panRed1 cat << '_EOF_' > panRed1.config.ra # Config parameters for makeGenomeDb.pl: db panRed1 clade worm genomeCladePriority 70 scientificName Panagrellus redivivus commonName P. redivivus assemblyDate Feb. 2013 assemblyShortLabel Pred3 assemblyLabel California Institute of Technology P. redivivus genome project orderKey 16020 mitoAcc KM192364.1 fastaFiles /hive/data/genomes/panRed1/ucsc/panRed1.fa.gz agpFiles /hive/data/genomes/panRed1/ucsc/panRed1.agp # qualFiles none dbDbSpeciesDir worm photoCreditURL http://www.wormbase.org/species/p_redivivus#4--10 photoCreditName WormBase WS240 ncbiGenomeId 16242 ncbiAssemblyId 541658 ncbiAssemblyName WS240/Pred3 ncbiBioProject 186477 genBankAccessionID GCA_000341325.1 taxId 6233 '_EOF_' # << happy emacs # verify sequence and AGP are OK: time (makeGenomeDb.pl -workhorse=hgwdev -dbHost=hgwdev -fileServer=hgwdev \ -stop=agp panRed1.config.ra) > agp.log 2>&1 # *** All done! (through the 'agp' step) # real 0m17.520s # then finish it off: time (makeGenomeDb.pl -workhorse=hgwdev -dbHost=hgwdev \ -fileServer=hgwdev -continue=db panRed1.config.ra) > db.log 2>&1 # real 0m49.181s # check in the trackDb files created and add to trackDb/makefile ############################################################################## # cpgIslands on UNMASKED sequence (DONE - 2015-07-01 - Hiram) mkdir /hive/data/genomes/panRed1/bed/cpgIslandsUnmasked cd /hive/data/genomes/panRed1/bed/cpgIslandsUnmasked time (doCpgIslands.pl -dbHost=hgwdev -bigClusterHub=ku -buildDir=`pwd` \ -tableName=cpgIslandExtUnmasked \ -maskedSeq=/hive/data/genomes/panRed1/panRed1.unmasked.2bit \ -workhorse=hgwdev -smallClusterHub=ku panRed1) > do.log 2>&1 # real 1m26.718s cat fb.panRed1.cpgIslandExtUnmasked.txt # 5218407 bases of 62228262 (8.386%) in intersection ############################################################################# # cytoBandIdeo - (DONE - 2015-07-01 - Hiram) mkdir /hive/data/genomes/panRed1/bed/cytoBand cd /hive/data/genomes/panRed1/bed/cytoBand makeCytoBandIdeo.csh panRed1 ######################################################################### # ucscToINSDC table/track (DONE - 2015-07-09 - Hiram) mkdir /hive/data/genomes/panRed1/bed/ucscToINSDC cd /hive/data/genomes/panRed1/bed/ucscToINSDC # find accession name for chrM grep chrM ../../*.agp # chrM 1 17089 2875 F KM192364.1 1 17089 + # use that as second argument here: ~/kent/src/hg/utils/automation/ucscToINSDC.sh \ ../../genbank/GCA_*assembly_structure/Primary_Assembly KM192364.1 awk '{printf "%s\t0\t%d\n", $1,$2}' ../../chrom.sizes \ | sort > name.coordinate.tab # eliminate the v1 from what would have been the UCSC names from genbank: sed -e 's/v1//;' ucscToINSDC.txt \ | join name.coordinate.tab - | tr '[ ]' '[\t]' \ > ucscToINSDC.bed # verify all names are coming through, should be same line count: wc -l * # 941 name.coordinate.tab # 941 ucscToINSDC.bed # 941 ucscToINSDC.txt cut -f1 ucscToINSDC.bed | awk '{print length($0)}' | sort -n | tail -1 # 12 # use the 12 in this sed sed -e "s/21/12/" $HOME/kent/src/hg/lib/ucscToINSDC.sql \ | hgLoadSqlTab panRed1 ucscToINSDC stdin ucscToINSDC.bed checkTableCoords panRed1 # should cover %100 entirely: featureBits -countGaps panRed1 ucscToINSDC # 65110236 bases of 65110236 (100.000%) in intersection ######################################################################### # fixup search rule for assembly track/gold table (DONE - 2015-07-01 - Hiram) hgsql -N -e "select frag from gold;" panRed1 | sort | head -3 AOMH01000001_1 AOMH01000002_1 AOMH01000003_1 hgsql -N -e "select frag from gold;" panRed1 | sort | tail -3 KB455574_8 KB455574_9 KM192364.1 # verify this rule will find them all or eliminate them all: hgsql -N -e "select frag from gold;" panRed1 | wc -l # 5978 hgsql -N -e "select frag from gold;" panRed1 \ | egrep -e '[AK][BMO][MH0-9]*([_\.][0-9]*)?' \ | wc -l # 5978 hgsql -N -e "select frag from gold;" panRed1 \ | egrep -v -e '[AK][BMO][MH0-9]*([_\.][0-9]*)?' | wc -l # 0 # hence, add to trackDb/worm/panRed1/trackDb.ra searchTable gold shortCircuit 1 termRegex [AK][BMO][MH0-9]*([_\.][0-9]*)? query select chrom,chromStart,chromEnd,frag from %s where frag like '%s%%' searchPriority 8 ########################################################################## # running repeat masker (DONE - 2015-07-01 - Hiram) mkdir /hive/data/genomes/panRed1/bed/repeatMasker cd /hive/data/genomes/panRed1/bed/repeatMasker time (doRepeatMasker.pl -buildDir=`pwd` \ -bigClusterHub=ku -dbHost=hgwdev -workhorse=hgwdev \ -smallClusterHub=ku panRed1) > do.log 2>&1 # real 30m48.149s # fixed a bug in the doLoad.bash script, then continuing: time (doRepeatMasker.pl -buildDir=`pwd` \ -bigClusterHub=ku -dbHost=hgwdev -workhorse=hgwdev \ -continue=cleanup -smallClusterHub=ku panRed1) > cleanup.log 2>&1 # real 0m10.772s cat faSize.rmsk.txt # 65110236 bases (3020128 N's 62090108 real 61787614 upper # 302494 lower) in 941 sequences in 1 files # Total size: mean 69192.6 sd 150304.4 min 362 (AOMH01000403) # max 2280433 (KB455460) median 12743 # %0.46 masked total, %0.49 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 panRed1 rmsk # 302575 bases of 65110236 (0.465%) in intersection # real 0m0.395s # 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 - 2015-07-01 - Hiram) mkdir /hive/data/genomes/panRed1/bed/simpleRepeat cd /hive/data/genomes/panRed1/bed/simpleRepeat time (doSimpleRepeat.pl -buildDir=`pwd` -bigClusterHub=ku \ -dbHost=hgwdev -workhorse=hgwdev -smallClusterHub=ku \ panRed1) > do.log 2>&1 # real 3m1.956s time (doSimpleRepeat.pl -buildDir=`pwd` -bigClusterHub=ku \ -dbHost=hgwdev -workhorse=hgwdev -smallClusterHub=ku \ -continue=cleanup panRed1) > cleanup.log 2>&1 cat fb.simpleRepeat # 756466 bases of 62228262 (1.216%) in intersection # using the Window Masker result as indicated below ########################################################################## # CREATE MICROSAT TRACK (DONE - 2015-07-01 - Hiram) ssh hgwdev mkdir /cluster/data/panRed1/bed/microsat cd /cluster/data/panRed1/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 panRed1 microsat microsat.bed # microsat.bed appears to be empty # there are none ########################################################################## ## WINDOWMASKER (DONE - 2015-07-01 - Hiram) mkdir /hive/data/genomes/panRed1/bed/windowMasker cd /hive/data/genomes/panRed1/bed/windowMasker time (doWindowMasker.pl -buildDir=`pwd` -workhorse=hgwdev \ -dbHost=hgwdev panRed1) > do.log 2>&1 # real 2m57.621s # Masking statistics cat faSize.panRed1.cleanWMSdust.txt # 65110236 bases (3020128 N's 62090108 real 53046172 upper # 9043936 lower) in 941 sequences in 1 files # Total size: mean 69192.6 sd 150304.4 min 362 (AOMH01000403) # max 2280433 (KB455460) median 12743 # %13.89 masked total, %14.57 masked real cat fb.panRed1.rmsk.windowmaskerSdust.txt # 167894 bases of 65110236 (0.258%) in intersection # using this Window Masker result for final masking:: cd /hive/data/genomes/panRed1 # you can safely ignore the warning about fields >= 13 twoBitMask bed/windowMasker/panRed1.cleanWMSdust.2bit \ -add bed/simpleRepeat/trfMask.bed panRed1.2bit # measure the final masking: twoBitToFa panRed1.2bit stdout | faSize stdin > faSize.panRed1.2bit.txt cat faSize.panRed1.2bit.txt # 65110236 bases (3020128 N's 62090108 real 53041454 upper # 9048654 lower) in 941 sequences in 1 files # Total size: mean 69192.6 sd 150304.4 min 362 (AOMH01000403) # max 2280433 (KB455460) median 12743 # %13.90 masked total, %14.57 masked real # and reset the symlink rm /gbdb/panRed1/panRed1.2bit ln -s /hive/data/genomes/panRed1/panRed1.2bit /gbdb/panRed1/panRed1.2bit ########################################################################## # cpgIslands - (DONE - 2015-07-01 - Hiram) mkdir /hive/data/genomes/panRed1/bed/cpgIslands cd /hive/data/genomes/panRed1/bed/cpgIslands time (doCpgIslands.pl -dbHost=hgwdev -bigClusterHub=ku \ -workhorse=hgwdev -smallClusterHub=ku panRed1) > do.log 2>&1 & # real 1m21.903s cat fb.panRed1.cpgIslandExt.txt # 3948577 bases of 62228262 (6.345%) in intersection ######################################################################### # augustus - (DONE - 2015-07-09 - Hiram) mkdir /hive/data/genomes/panRed1/bed/augustus cd /hive/data/genomes/panRed1/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 panRed1) > do.log 2>&1 # real 13m23.195s cat fb.panRed1.augustusGene.txt # 24225124 bases of 62228262 (38.929%) in intersection ######################################################################### # genscan - (DONE - 2015-07-01 - Hiram) mkdir /hive/data/genomes/panRed1/bed/genscan cd /hive/data/genomes/panRed1/bed/genscan time (doGenscan.pl -buildDir=`pwd` -workhorse=hgwdev -dbHost=hgwdev \ -bigClusterHub=ku panRed1) > do.log 2>&1 # real 2m58.421s cat fb.panRed1.genscan.txt # 13419606 bases of 62228262 (21.565%) in intersection cat fb.panRed1.genscanSubopt.txt # 9038121 bases of 62228262 (14.524%) in intersection ######################################################################## # Create kluster run files (TBD - 2015-03-24 - Hiram) cd /hive/data/genomes/panRed1 # numerator is panRed1 gapless bases "real" as reported by: head -1 faSize.panRed1.2bit.txt # 2053849526 bases (76078142 N's 1977771384 real 1208345365 upper # 76942601 lower) in 25187 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 \( 1977771384 / 2861349177 \) \* 1024 # ( 1977771384 / 2861349177 ) * 1024 = 707.791245 # ==> use -repMatch=700 according to size scaled down from 1024 for human. # and rounded down to nearest 50 cd /hive/data/genomes/panRed1 time blat panRed1.2bit \ /dev/null /dev/null -tileSize=11 -makeOoc=jkStuff/panRed1.11.ooc \ -repMatch=700 # Wrote 23756 overused 11-mers to jkStuff/panRed1.11.ooc # real 0m32.961s # 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;' panRed1 # | 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 panRed1 jkStuff/panRed1.nonBridged.lft \ # -bedFile=jkStuff/panRed1.nonBridged.bed # hgsql -N \ # -e 'select * from gap where bridge="no" order by size;' panRed1 \ # | 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: 25187, total size: 2053849526, one half size: 1026924763 # cumulative N50 count contig contig size # 1026149130 545 KN906416v1 1073586 # 1026924763 one half size # 1027218231 546 KN906384v1 1069101 ############################################################################# # 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 # Nanorana parkeri 3 0 0 # Nanorana pleskei 3 0 0 # Nanorana yunnanensis 1 0 0 # edit etc/genbank.conf to add panRed1 just before xenTro7 # panRed1 (tibetan frog) panRed1.serverGenome = /hive/data/genomes/panRed1/panRed1.2bit panRed1.clusterGenome = /hive/data/genomes/panRed1/panRed1.2bit panRed1.ooc = /hive/data/genomes/panRed1/jkStuff/panRed1.11.ooc panRed1.lift = no panRed1.perChromTables = no panRed1.refseq.mrna.xeno.pslCDnaFilter = ${lowCover.refseq.mrna.xeno.pslCDnaFilter} panRed1.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter} panRed1.genbank.mrna.xeno.pslCDnaFilter = ${lowCover.genbank.mrna.xeno.pslCDnaFilter} panRed1.genbank.est.native.pslCDnaFilter = ${lowCover.genbank.est.native.pslCDnaFilter} panRed1.genbank.est.xeno.pslCDnaFilter = ${lowCover.genbank.est.xeno.pslCDnaFilter} panRed1.downloadDir = panRed1 panRed1.refseq.mrna.native.load = no panRed1.refseq.mrna.xeno.load = yes panRed1.refseq.mrna.xeno.loadDesc = yes panRed1.genbank.mrna.native.load = no panRed1.genbank.mrna.native.loadDesc = no panRed1.genbank.mrna.xeno.load = yes panRed1.genbank.mrna.xeno.loadDesc = yes panRed1.genbank.est.native.load = no panRed1.genbank.est.native.loadDesc = no # panRed1.upstreamGeneTbl = ensGene # Edit src/lib/gbGenome.c to add new species. git commit -m "Added nanPar Nanorana parkeri refs #15056" \ etc/genbank.conf src/lib/gbGenome.c git push # update /cluster/data/genbank/etc/: make etc-update # update /cluster/data/genbank/bin/: make install-server screen # control this business with a screen since it takes a while cd /cluster/data/genbank time ./bin/gbAlignStep -initial panRed1 # logFile: var/build/logs/2015.05.27-15:45:35.panRed1.initalign.log # real 1651m57.350s # To re-do, rm the dir first: # /cluster/data/genbank/work/initial.panRed1 # load database when finished ssh hgwdev cd /cluster/data/genbank time ./bin/gbDbLoadStep -drop -initialLoad panRed1 # logFile: var/dbload/hgwdev/logs/2015.06.09-14:34:12.panRed1.dbload.log # real 128m32.009s # enable daily alignment and update of hgwdev cd ~/kent/src/hg/makeDb/genbank git pull # add panRed1 to: # vi etc/align.dbs etc/hgwdev.dbs git commit -m "Added panRed1 - Tibetan frog refs #15056" \ 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=panRed1 -tableCoverage all.joiner joinerCheck -database=panRed1 -times all.joiner joinerCheck -database=panRed1 -keys all.joiner cd /hive/data/genomes/panRed1 time makeDownloads.pl panRed1 > downloads.log 2>&1 # real 13m42.027s # now ready for pushQ entry mkdir /hive/data/genomes/panRed1/pushQ cd /hive/data/genomes/panRed1/pushQ makePushQSql.pl panRed1 > panRed1.pushQ.sql 2> stderr.out # check for errors in stderr.out, some are OK, e.g.: # WARNING: hgwdev does not have /gbdb/panRed1/wib/gc5Base.wib # WARNING: hgwdev does not have /gbdb/panRed1/wib/quality.wib # WARNING: hgwdev does not have /gbdb/panRed1/bbi/qualityBw/quality.bw # WARNING: panRed1 does not have seq # WARNING: panRed1 does not have extFile # WARNING: panRed1 does not have estOrientInfo # WARNING: panRed1 does not have mrnaOrientInfo # copy it to hgwbeta scp -p panRed1.pushQ.sql qateam@hgwbeta:/tmp ssh qateam@hgwbeta "./bin/x86_64/hgsql qapushq < /tmp/panRed1.pushQ.sql" # in that pushQ entry walk through each entry and see if the # sizes will set properly ######################################################################### # improve common name (DONE - 2015-07-24 - Hiram) hgsql -e 'update dbDb set organism="Microworm" where name="panRed1";' hgcentraltest #############################################################################