# for emacs: -*- mode: sh; -*- # This file describes the browser build for # Trichuris suis/whipworm 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/triSui1/genbank cd /hive/data/genomes/triSui1/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/triSui1/ws245 cd /hive/data/genomes/triSui1/ws245 wget --no-parent --timestamping -m -nH --cut-dirs=6 \ ftp://ftp.sanger.ac.uk/pub/wormbase/releases/WS245/species/PRJNA208415 wget --no-parent --timestamping -m -nH --cut-dirs=6 \ ftp://ftp.sanger.ac.uk/pub/wormbase/releases/WS245/species/PRJNA208416 mkdir /hive/data/genomes/triSui1/ucsc cd /hive/data/genomes/triSui1/ucsc zcat ../genbank/GCA_000701005.1_Tsuis_adult_male_v1.0_assembly_structure/Primary_Assembly/unplaced_scaffolds/FASTA/unplaced.scaf.fna.gz \ | sed -e 's/.1 Trichuris .*/v1/;' | gzip -c > triSui1.fa.gz zcat ../genbank/GCA_000701005.1_Tsuis_adult_male_v1.0_assembly_structure/Primary_Assembly/unplaced_scaffolds/AGP/unplaced.scaf.agp.gz \ | sed -e 's/\.1/v1/;' > triSui1.agp # obtain photo, CDC public domain photo mkdir /hive/data/genomes/triSui1/photo cd /hive/data/genomes/triSui1/photo wget --timestamping \ http://www.cdc.gov/parasites/images/whipworm/home_page_image_whipworm.jpg convert -geometry 400x300 home_page_image_whipworm.jpg Trichuris_suis.jpg # check into source tree # src/hg/htdocs/images/Trichuris_suis.jpg # and copy to /usr/local/apache/htdocs/images/Trichuris_suis.jpg ############################################################################# # Initial database build (DONE - 2015-07-10 - Hiram) cd /hive/data/genomes/triSui1 cat << '_EOF_' > triSui1.config.ra # Config parameters for makeGenomeDb.pl: db triSui1 clade worm genomeCladePriority 68 scientificName Trichuris suis commonName Whipworm assemblyDate Jul. 2014 assemblyLabel University of Melboure T. suis (male) genome project assemblyShortLabel WS243/T. suis DCEP-RM93M male orderKey 23200 mitoAcc GU070737.1 fastaFiles /hive/data/genomes/triSui1/ucsc/triSui1.fa.gz agpFiles /hive/data/genomes/triSui1/ucsc/triSui1.agp # qualFiles none dbDbSpeciesDir worm photoCreditURL http://www.cdc.gov/parasites/whipworm/ photoCreditName Centers for Disease Control and Prevention ncbiGenomeId 13427 ncbiAssemblyId 205451 ncbiAssemblyName WS243/Tsuis_adult_male_v1.0 ncbiBioProject 208415 genBankAccessionID GCA_000701005.1 taxId 68888 '_EOF_' # << happy emacs # verify sequence and AGP are OK: time (makeGenomeDb.pl -workhorse=hgwdev -dbHost=hgwdev -fileServer=hgwdev \ -stop=agp triSui1.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 triSui1.config.ra) > db.log 2>&1 # real 0m53.141s # check in the trackDb files created and add to trackDb/makefile ############################################################################## # cpgIslands on UNMASKED sequence (DONE - 2015-07-10 - Hiram) mkdir /hive/data/genomes/triSui1/bed/cpgIslandsUnmasked cd /hive/data/genomes/triSui1/bed/cpgIslandsUnmasked time (doCpgIslands.pl -dbHost=hgwdev -bigClusterHub=ku -buildDir=`pwd` \ -tableName=cpgIslandExtUnmasked \ -maskedSeq=/hive/data/genomes/triSui1/triSui1.unmasked.2bit \ -workhorse=hgwdev -smallClusterHub=ku triSui1) > do.log 2>&1 # real 4m37.436s cat fb.triSui1.cpgIslandExtUnmasked.txt # 4053516 bases of 71825323 (5.644%) in intersection ############################################################################# # cytoBandIdeo - (DONE - 2015-07-10 - Hiram) mkdir /hive/data/genomes/triSui1/bed/cytoBand cd /hive/data/genomes/triSui1/bed/cytoBand makeCytoBandIdeo.csh triSui1 ######################################################################### # ucscToINSDC table/track (DONE - 2015-07-10 - Hiram) mkdir /hive/data/genomes/triSui1/bed/ucscToINSDC cd /hive/data/genomes/triSui1/bed/ucscToINSDC # find the chrM accession: grep chrM ../../*.agp # chrM 1 14436 2 F GU070737.1 1 14436 + # use that as the second argument here: ~/kent/src/hg/utils/automation/ucscToINSDC.sh \ ../../genbank/GCA_000701005.1_Tsuis_adult_male_v1.0_assembly_structure/Primary_Assembly GU070737.1 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 * # 4293 name.coordinate.tab # 4293 ucscToINSDC.bed # 4293 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 triSui1 ucscToINSDC stdin ucscToINSDC.bed checkTableCoords triSui1 # should cover %100 entirely: featureBits -countGaps triSui1 ucscToINSDC # 74248995 bases of 74248995 (100.000%) in intersection ######################################################################### # fixup search rule for assembly track/gold table (DONE - 2015-07-10 - Hiram) hgsql -N -e "select frag from gold;" triSui1 | sort | head -3 GU070737.1 JMHY01000001.1 JMHY01000002.1 hgsql -N -e "select frag from gold;" triSui1 | sort | tail -2 JMHY01006464.1 JMHY01006465.1 # verify this rule will find them all or eliminate them all: hgsql -N -e "select frag from gold;" triSui1 | wc -l # 6466 hgsql -N -e "select frag from gold;" triSui1 \ | egrep -e '(GU070737|JMHY0100)[0-9]*(\.1)?' | wc -l # 6466 hgsql -N -e "select frag from gold;" triSui1 \ | egrep -v -e '(GU070737|JMHY0100)[0-9]*(\.1)?' | wc -l # 0 # hence, add to trackDb/worm/triSui1/trackDb.ra searchTable gold shortCircuit 1 termRegex (GU070737|JMHY0100)[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/triSui1/bed/repeatMasker cd /hive/data/genomes/triSui1/bed/repeatMasker time (doRepeatMasker.pl -buildDir=`pwd` \ -bigClusterHub=ku -dbHost=hgwdev -workhorse=hgwdev \ -smallClusterHub=ku triSui1) > do.log 2>&1 # real 153m32.056s cat faSize.rmsk.txt # 74248995 bases (2423806 N's 71825189 real 71306874 upper 518315 lower) # in 4293 sequences in 1 files # Total size: mean 17295.4 sd 100439.5 min 201 (KL367473v1) # max 1594463 (KL363182v1) median 314 # %0.70 masked total, %0.72 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 triSui1 rmsk # 518334 bases of 74248995 (0.698%) in intersection # real 0m1.256s ########################################################################## # running simple repeat (DONE - 2015-07-10 - Hiram) mkdir /hive/data/genomes/triSui1/bed/simpleRepeat cd /hive/data/genomes/triSui1/bed/simpleRepeat time (doSimpleRepeat.pl -buildDir=`pwd` -bigClusterHub=ku \ -dbHost=hgwdev -workhorse=hgwdev -smallClusterHub=ku \ triSui1) > do.log 2>&1 # real 3m56.113s cat fb.simpleRepeat # 1984238 bases of 71825323 (2.763%) in intersection # using the Window Masker result as indicated below ########################################################################## # CREATE MICROSAT TRACK (DONE - 2015-07-15 - Hiram) ssh hgwdev mkdir /cluster/data/triSui1/bed/microsat cd /cluster/data/triSui1/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 triSui1 microsat microsat.bed # Read 310 elements of size 4 from microsat.bed ########################################################################## ## WINDOWMASKER (DONE - 2015-07-15 - Hiram) mkdir /hive/data/genomes/triSui1/bed/windowMasker cd /hive/data/genomes/triSui1/bed/windowMasker time (doWindowMasker.pl -buildDir=`pwd` -workhorse=hgwdev \ -dbHost=hgwdev triSui1) > do.log 2>&1 # real 3m14.998s # Masking statistics cat faSize.triSui1.cleanWMSdust.txt # 74248995 bases (2423806 N's 71825189 real 62955556 upper 8869633 lower) # in 4293 sequences in 1 files # Total size: mean 17295.4 sd 100439.5 min 201 (KL367473v1) # max 1594463 (KL363182v1) median 314 # %11.95 masked total, %12.35 masked real cat fb.triSui1.rmsk.windowmaskerSdust.txt # 410663 bases of 74248995 (0.553%) in intersection # using this Window Masker result for final masking:: cd /hive/data/genomes/triSui1 # you can safely ignore the warning about fields >= 13 twoBitMask bed/windowMasker/triSui1.cleanWMSdust.2bit \ -add bed/simpleRepeat/trfMask.bed triSui1.2bit # measure the final masking: twoBitToFa triSui1.2bit stdout | faSize stdin > faSize.triSui1.2bit.txt cat faSize.triSui1.2bit.txt # 74248995 bases (2423806 N's 71825189 real 62949616 upper 8875573 lower) # in 4293 sequences in 1 files # Total size: mean 17295.4 sd 100439.5 min 201 (KL367473v1) # max 1594463 (KL363182v1) median 314 # %11.95 masked total, %12.36 masked real # and reset the symlink rm /gbdb/triSui1/triSui1.2bit ln -s /hive/data/genomes/triSui1/triSui1.2bit /gbdb/triSui1/triSui1.2bit ########################################################################## # cpgIslands - (DONE - 2015-07-15 - Hiram) mkdir /hive/data/genomes/triSui1/bed/cpgIslands cd /hive/data/genomes/triSui1/bed/cpgIslands time (doCpgIslands.pl -dbHost=hgwdev -bigClusterHub=ku \ -workhorse=hgwdev -smallClusterHub=ku triSui1) > do.log 2>&1 & # real 55m19.060s cat fb.triSui1.cpgIslandExt.txt # 3089138 bases of 71825323 (4.301%) in intersection ######################################################################### # augustus - (DONE - 2015-07-15 - Hiram) mkdir /hive/data/genomes/triSui1/bed/augustus cd /hive/data/genomes/triSui1/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 triSui1) > do.log 2>&1 & # real 39m50.787s cat fb.triSui1.augustusGene.txt # 15594049 bases of 71825323 (21.711%) in intersection ######################################################################### # genscan - (DONE - 2015-07-15 - Hiram) mkdir /hive/data/genomes/triSui1/bed/genscan cd /hive/data/genomes/triSui1/bed/genscan time (doGenscan.pl -buildDir=`pwd` -workhorse=hgwdev -dbHost=hgwdev \ -bigClusterHub=ku triSui1) > do.log 2>&1 # real 45m29.041s cat fb.triSui1.genscan.txt # 9305968 bases of 71825323 (12.956%) in intersection cat fb.triSui1.genscanSubopt.txt # 7502974 bases of 71825323 (10.446%) in intersection ######################################################################## # Create kluster run files (TBD - 2015-07-08 - Hiram) cd /hive/data/genomes/triSui1 # numerator is triSui1 gapless bases "real" as reported by: head -1 faSize.triSui1.2bit.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/triSui1 time blat triSui1.2bit \ /dev/null /dev/null -tileSize=11 -makeOoc=jkStuff/triSui1.11.ooc \ -repMatch=100 # Wrote 8527 overused 11-mers to jkStuff/triSui1.11.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;' triSui1 \ | 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 triSui1 jkStuff/triSui1.nonBridged.lft \ -bedFile=jkStuff/triSui1.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 triSui1 just before priPac1 # triSui1 (P. pacificus) triSui1.serverGenome = /hive/data/genomes/triSui1/triSui1.2bit triSui1.clusterGenome = /hive/data/genomes/triSui1/triSui1.2bit triSui1.ooc = /hive/data/genomes/triSui1/jkStuff/triSui1.11.ooc triSui1.lift = /hive/data/genomes/triSui1/jkStuff/triSui1.nonBridged.lft triSui1.refseq.mrna.native.pslCDnaFilter = ${ordered.refseq.mrna.native.pslCDnaFilter} triSui1.refseq.mrna.xeno.pslCDnaFilter = ${ordered.refseq.mrna.xeno.pslCDnaFilter} triSui1.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter} triSui1.genbank.mrna.xeno.pslCDnaFilter = ${ordered.genbank.mrna.xeno.pslCDnaFilter} triSui1.genbank.est.native.pslCDnaFilter = ${ordered.genbank.est.native.pslCDnaFilter} triSui1.refseq.mrna.native.load = yes triSui1.refseq.mrna.xeno.load = yes triSui1.refseq.mrna.xeno.loadDesc = yes # DO NOT NEED genbank.mrna.xeno except for human, mouse triSui1.genbank.mrna.xeno.load = no triSui1.genbank.est.native.load = yes triSui1.genbank.est.native.loadDesc = no triSui1.downloadDir = triSui1 triSui1.perChromTables = no git commit -m "Added triSui1 - 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 triSui1 # logFile: var/build/logs/2015.07.02-11:39:01.triSui1.initalign.log # real 91m20.362s # To re-do, rm the dir first: # /cluster/data/genbank/work/initial.triSui1 # load database when finished ssh hgwdev cd /cluster/data/genbank time ./bin/gbDbLoadStep -drop -initialLoad triSui1 # logFile: var/dbload/hgwdev/logs/2015.07.06-09:51:31.triSui1.dbload.log # real 18m34.687s # enable daily alignment and update of hgwdev cd ~/kent/src/hg/makeDb/genbank git pull # add triSui1 to: # vi etc/align.dbs etc/hgwdev.dbs git commit -m "Added triSui1 - 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=triSui1 -tableCoverage all.joiner joinerCheck -database=triSui1 -times all.joiner joinerCheck -database=triSui1 -keys all.joiner cd /hive/data/genomes/triSui1 time makeDownloads.pl triSui1 > downloads.log 2>&1 # real 13m42.027s # now ready for pushQ entry mkdir /hive/data/genomes/triSui1/pushQ cd /hive/data/genomes/triSui1/pushQ makePushQSql.pl triSui1 > triSui1.pushQ.sql 2> stderr.out # check for errors in stderr.out, some are OK, e.g.: # WARNING: hgwdev does not have /gbdb/triSui1/wib/gc5Base.wib # WARNING: hgwdev does not have /gbdb/triSui1/wib/quality.wib # WARNING: hgwdev does not have /gbdb/triSui1/bbi/qualityBw/quality.bw # WARNING: triSui1 does not have seq # WARNING: triSui1 does not have extFile # WARNING: triSui1 does not have estOrientInfo # WARNING: triSui1 does not have mrnaOrientInfo # copy it to hgwbeta scp -p triSui1.pushQ.sql qateam@hgwbeta:/tmp ssh qateam@hgwbeta "./bin/x86_64/hgsql qapushq < /tmp/triSui1.pushQ.sql" # in that pushQ entry walk through each entry and see if the # sizes will set properly #############################################################################