# for emacs: -*- mode: sh; -*- # This file describes the browser build for Trichinella spiralis 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/triSpi1/genbank cd /hive/data/genomes/triSpi1/genbank time rsync -L -a -P \ rsync://ftp.ncbi.nlm.nih.gov/genomes/genbank/invertebrate/Trichinella_spiralis/all_assembly_versions/GCA_000181795.2_Trichinella_spiralis-3.7.1/ ./ # sent 394 bytes received 81911524 bytes 7122775.48 bytes/sec # total size is 81899323 speedup is 1.00 # real 0m10.375s mkdir -p /hive/data/genomes/triSpi1/ws245 cd /hive/data/genomes/triSpi1/ws245 wget --no-parent --timestamping -m -nH --cut-dirs=6 \ ftp://ftp.sanger.ac.uk/pub/wormbase/releases/WS245/species/PRJNA12603 mkdir /hive/data/genomes/triSpi1/ucsc cd /hive/data/genomes/triSpi1/ucsc zcat ../genbank/GCA_000181795.2_Trichinella_spiralis-3.7.1_assembly_structure/Primary_Assembly/unplaced_scaffolds/FASTA/unplaced.scaf.fna.gz \ | sed -e 's/.1 Trichinella .*/v1/;' | gzip -c > triSpi1.fa.gz zcat ../genbank/GCA_000181795.2_Trichinella_spiralis-3.7.1_assembly_structure/Primary_Assembly/unplaced_scaffolds/AGP/unplaced.scaf.agp.gz \ | sed -e 's/\.1/v1/;' > triSpi1.agp # obtain photo, CDC public domain photo mkdir /hive/data/genomes/triSpi1/photo cd /hive/data/genomes/triSpi1/photo wget --timestamping \ http://www.cdc.gov/dpdx/images/trichinellosis/Trichinella_larvaeF.jpg # it is already 300x300 check in to # src/hg/htdocs/images/Trichinella_spiralis.jpg # and copy to /usr/local/apache/htdocs/images/Trichinella_spiralis.jpg ############################################################################# # Initial database build (DONE - 2015-07-10 - Hiram) cd /hive/data/genomes/triSpi1 cat << '_EOF_' > triSpi1.config.ra # Config parameters for makeGenomeDb.pl: db triSpi1 clade worm genomeCladePriority 68 scientificName Trichinella spiralis commonName T. spiralis assemblyDate Jan. 2011 assemblyLabel WashU School of Medicine T. spiralis genome project assemblyShortLabel WS225/Trichinella_spiralis-3.7.1 orderKey 20030 mitoAcc AF293969.1 fastaFiles /hive/data/genomes/triSpi1/ucsc/triSpi1.fa.gz agpFiles /hive/data/genomes/triSpi1/ucsc/triSpi1.agp # qualFiles none dbDbSpeciesDir worm photoCreditURL http://www.cdc.gov/dpdx/trichinellosis/gallery.html#larvaebear photoCreditName Centers for Disease Control and Prevention ncbiGenomeId 238 ncbiAssemblyId 245458 ncbiAssemblyName WS225/Trichinella_spiralis-3.7.1 ncbiBioProject 12603 genBankAccessionID GCA_000181795.2 taxId 6334 '_EOF_' # << happy emacs # verify sequence and AGP are OK: time (makeGenomeDb.pl -workhorse=hgwdev -dbHost=hgwdev -fileServer=hgwdev \ -stop=agp triSpi1.config.ra) > agp.log 2>&1 # *** All done! (through the 'agp' step) # real 0m20.536s # then finish it off: time (makeGenomeDb.pl -workhorse=hgwdev -dbHost=hgwdev \ -fileServer=hgwdev -continue=db triSpi1.config.ra) > db.log 2>&1 # real 0m51.541s # check in the trackDb files created and add to trackDb/makefile ############################################################################## # cpgIslands on UNMASKED sequence (DONE - 2015-07-10 - Hiram) mkdir /hive/data/genomes/triSpi1/bed/cpgIslandsUnmasked cd /hive/data/genomes/triSpi1/bed/cpgIslandsUnmasked time (doCpgIslands.pl -dbHost=hgwdev -bigClusterHub=ku -buildDir=`pwd` \ -tableName=cpgIslandExtUnmasked \ -maskedSeq=/hive/data/genomes/triSpi1/triSpi1.unmasked.2bit \ -workhorse=hgwdev -smallClusterHub=ku triSpi1) > do.log 2>&1 # real 5m36.177s cat fb.triSpi1.cpgIslandExtUnmasked.txt # 2557009 bases of 58558192 (4.367%) in intersection ############################################################################# # cytoBandIdeo - (DONE - 2015-07-10 - Hiram) mkdir /hive/data/genomes/triSpi1/bed/cytoBand cd /hive/data/genomes/triSpi1/bed/cytoBand makeCytoBandIdeo.csh triSpi1 ######################################################################### # ucscToINSDC table/track (DONE - 2015-07-10 - Hiram) mkdir /hive/data/genomes/triSpi1/bed/ucscToINSDC cd /hive/data/genomes/triSpi1/bed/ucscToINSDC # find the chrM accession: grep chrM ../../*.agp # chrM 1 16706 2 F AF293969.1 1 16706 + # use that as the second argument here: ~/kent/src/hg/utils/automation/ucscToINSDC.sh \ ../../genbank/GCA_*assembly_structure/Primary_Assembly AF293969.1 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 * # 6864 name.coordinate.tab # 6864 ucscToINSDC.bed # 6864 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 triSpi1 ucscToINSDC stdin ucscToINSDC.bed checkTableCoords triSpi1 # should cover %100 entirely: featureBits -countGaps triSpi1 ucscToINSDC # 63542128 bases of 63542128 (100.000%) in intersection ######################################################################### # fixup search rule for assembly track/gold table (DONE - 2015-07-10 - Hiram) hgsql -N -e "select frag from gold;" triSpi1 | sort | head -3 ABIR02000001.1 ABIR02000002.1 ABIR02000003.1 hgsql -N -e "select frag from gold;" triSpi1 | sort | tail -2 ABIR02009267.1 AF293969.1 # verify this rule will find them all or eliminate them all: hgsql -N -e "select frag from gold;" triSpi1 | wc -l # 9268 hgsql -N -e "select frag from gold;" triSpi1 \ | egrep -e '(ABIR0200|AF293969)[0-9]*(\.1)?' | wc -l # 9268 hgsql -N -e "select frag from gold;" triSpi1 \ | egrep -v -e '(ABIR0200|AF293969)[0-9]*(\.1)?' | wc -l # 0 # hence, add to trackDb/worm/triSpi1/trackDb.ra searchTable gold shortCircuit 1 termRegex (ABIR0200|AF293969)[0-9]*(\.1)? query select chrom,chromStart,chromEnd,frag from %s where frag like '%s%%' searchPriority 8 ########################################################################## # running repeat masker (DONE - 2015-07-10 - Hiram) mkdir /hive/data/genomes/triSpi1/bed/repeatMasker cd /hive/data/genomes/triSpi1/bed/repeatMasker time (doRepeatMasker.pl -buildDir=`pwd` \ -bigClusterHub=ku -dbHost=hgwdev -workhorse=hgwdev \ -smallClusterHub=ku triSpi1) > do.log 2>&1 # real 35m3.117s cat faSize.rmsk.txt # 63542128 bases (4986988 N's 58555140 real 56390244 upper 2164896 lower) # in 6864 sequences in 1 files # Total size: mean 9257.3 sd 248572.9 min 139 (GL624204v1) # max 12041450 (GL622787v1) median 1071 # %3.41 masked total, %3.70 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 triSpi1 rmsk # 2164933 bases of 63542128 (3.407%) in intersection # real 0m2.881s ########################################################################## # running simple repeat (DONE - 2015-07-10 - Hiram) mkdir /hive/data/genomes/triSpi1/bed/simpleRepeat cd /hive/data/genomes/triSpi1/bed/simpleRepeat time (doSimpleRepeat.pl -buildDir=`pwd` -bigClusterHub=ku \ -dbHost=hgwdev -workhorse=hgwdev -smallClusterHub=ku \ triSpi1) > do.log 2>&1 # real 5m3.124s cat fb.simpleRepeat # 717851 bases of 58558192 (1.226%) in intersection # using the Window Masker result as indicated below ########################################################################## # CREATE MICROSAT TRACK (DONE - 2015-07-15 - Hiram) ssh hgwdev mkdir /cluster/data/triSpi1/bed/microsat cd /cluster/data/triSpi1/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 triSpi1 microsat microsat.bed # Read 699 elements of size 4 from microsat.bed ########################################################################## ## WINDOWMASKER (DONE - 2015-07-15 - Hiram) mkdir /hive/data/genomes/triSpi1/bed/windowMasker cd /hive/data/genomes/triSpi1/bed/windowMasker time (doWindowMasker.pl -buildDir=`pwd` -workhorse=hgwdev \ -dbHost=hgwdev triSpi1) > do.log 2>&1 # real 4m15.661s # Masking statistics cat faSize.triSpi1.cleanWMSdust.txt # 63542128 bases (4986988 N's 58555140 real 38676889 upper 19878251 lower) # in 6864 sequences in 1 files # Total size: mean 9257.3 sd 248572.9 min 139 (GL624204v1) # max 12041450 (GL622787v1) median 1071 # %31.28 masked total, %33.95 masked real cat fb.triSpi1.rmsk.windowmaskerSdust.txt # 1699489 bases of 63542128 (2.675%) in intersection # using this Window Masker result for final masking:: cd /hive/data/genomes/triSpi1 # you can safely ignore the warning about fields >= 13 twoBitMask bed/windowMasker/triSpi1.cleanWMSdust.2bit \ -add bed/simpleRepeat/trfMask.bed triSpi1.2bit # measure the final masking: twoBitToFa triSpi1.2bit stdout | faSize stdin > faSize.triSpi1.2bit.txt cat faSize.triSpi1.2bit.txt # 63542128 bases (4986988 N's 58555140 real 38673309 upper 19881831 lower) # in 6864 sequences in 1 files # Total size: mean 9257.3 sd 248572.9 min 139 (GL624204v1) # max 12041450 (GL622787v1) median 1071 # %31.29 masked total, %33.95 masked real # and reset the symlink rm /gbdb/triSpi1/triSpi1.2bit ln -s /hive/data/genomes/triSpi1/triSpi1.2bit /gbdb/triSpi1/triSpi1.2bit ########################################################################## # cpgIslands - (DONE - 2015-07-15 - Hiram) mkdir /hive/data/genomes/triSpi1/bed/cpgIslands cd /hive/data/genomes/triSpi1/bed/cpgIslands time (doCpgIslands.pl -dbHost=hgwdev -bigClusterHub=ku \ -workhorse=hgwdev -smallClusterHub=ku triSpi1) > do.log 2>&1 & # real 15m51.807s cat fb.triSpi1.cpgIslandExt.txt # 2025345 bases of 58558192 (3.459%) in intersection ######################################################################### # augustus - (DONE - 2015-07-15 - Hiram) mkdir /hive/data/genomes/triSpi1/bed/augustus cd /hive/data/genomes/triSpi1/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 triSpi1) > do.log 2>&1 & # real 64m45.505s cat fb.triSpi1.augustusGene.txt # 8039688 bases of 58558192 (13.729%) in intersection ######################################################################### # genscan - (DONE - 2015-07-15 - Hiram) mkdir /hive/data/genomes/triSpi1/bed/genscan cd /hive/data/genomes/triSpi1/bed/genscan time (doGenscan.pl -buildDir=`pwd` -workhorse=hgwdev -dbHost=hgwdev \ -bigClusterHub=ku triSpi1) > do.log 2>&1 # real 10m7.962s cat fb.triSpi1.genscan.txt # 4576895 bases of 58558192 (7.816%) in intersection cat fb.triSpi1.genscanSubopt.txt # 973684 bases of 58558192 (1.663%) in intersection ######################################################################## # Create kluster run files (TBD - 2015-07-08 - Hiram) cd /hive/data/genomes/triSpi1 # numerator is triSpi1 gapless bases "real" as reported by: head -1 faSize.triSpi1.2bit.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/triSpi1 time blat triSpi1.2bit \ /dev/null /dev/null -tileSize=11 -makeOoc=jkStuff/triSpi1.11.ooc \ -repMatch=100 # Wrote 8527 overused 11-mers to jkStuff/triSpi1.11.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;' triSpi1 \ | 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 triSpi1 jkStuff/triSpi1.nonBridged.lft \ -bedFile=jkStuff/triSpi1.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 triSpi1 just before priPac1 # triSpi1 (P. pacificus) triSpi1.serverGenome = /hive/data/genomes/triSpi1/triSpi1.2bit triSpi1.clusterGenome = /hive/data/genomes/triSpi1/triSpi1.2bit triSpi1.ooc = /hive/data/genomes/triSpi1/jkStuff/triSpi1.11.ooc triSpi1.lift = /hive/data/genomes/triSpi1/jkStuff/triSpi1.nonBridged.lft triSpi1.refseq.mrna.native.pslCDnaFilter = ${ordered.refseq.mrna.native.pslCDnaFilter} triSpi1.refseq.mrna.xeno.pslCDnaFilter = ${ordered.refseq.mrna.xeno.pslCDnaFilter} triSpi1.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter} triSpi1.genbank.mrna.xeno.pslCDnaFilter = ${ordered.genbank.mrna.xeno.pslCDnaFilter} triSpi1.genbank.est.native.pslCDnaFilter = ${ordered.genbank.est.native.pslCDnaFilter} triSpi1.refseq.mrna.native.load = yes triSpi1.refseq.mrna.xeno.load = yes triSpi1.refseq.mrna.xeno.loadDesc = yes # DO NOT NEED genbank.mrna.xeno except for human, mouse triSpi1.genbank.mrna.xeno.load = no triSpi1.genbank.est.native.load = yes triSpi1.genbank.est.native.loadDesc = no triSpi1.downloadDir = triSpi1 triSpi1.perChromTables = no git commit -m "Added triSpi1 - 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 triSpi1 # logFile: var/build/logs/2015.07.02-11:39:01.triSpi1.initalign.log # real 91m20.362s # To re-do, rm the dir first: # /cluster/data/genbank/work/initial.triSpi1 # load database when finished ssh hgwdev cd /cluster/data/genbank time ./bin/gbDbLoadStep -drop -initialLoad triSpi1 # logFile: var/dbload/hgwdev/logs/2015.07.06-09:51:31.triSpi1.dbload.log # real 18m34.687s # enable daily alignment and update of hgwdev cd ~/kent/src/hg/makeDb/genbank git pull # add triSpi1 to: # vi etc/align.dbs etc/hgwdev.dbs git commit -m "Added triSpi1 - 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=triSpi1 -tableCoverage all.joiner joinerCheck -database=triSpi1 -times all.joiner joinerCheck -database=triSpi1 -keys all.joiner cd /hive/data/genomes/triSpi1 time makeDownloads.pl triSpi1 > downloads.log 2>&1 # real 13m42.027s # now ready for pushQ entry mkdir /hive/data/genomes/triSpi1/pushQ cd /hive/data/genomes/triSpi1/pushQ makePushQSql.pl triSpi1 > triSpi1.pushQ.sql 2> stderr.out # check for errors in stderr.out, some are OK, e.g.: # WARNING: hgwdev does not have /gbdb/triSpi1/wib/gc5Base.wib # WARNING: hgwdev does not have /gbdb/triSpi1/wib/quality.wib # WARNING: hgwdev does not have /gbdb/triSpi1/bbi/qualityBw/quality.bw # WARNING: triSpi1 does not have seq # WARNING: triSpi1 does not have extFile # WARNING: triSpi1 does not have estOrientInfo # WARNING: triSpi1 does not have mrnaOrientInfo # copy it to hgwbeta scp -p triSpi1.pushQ.sql qateam@hgwbeta:/tmp ssh qateam@hgwbeta "./bin/x86_64/hgsql qapushq < /tmp/triSpi1.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="Trichina worm" where name="triSpi1";' hgcentraltest #############################################################################