# for emacs: -*- mode: sh; -*- # This file describes browser build for the aptMan1 # Apteryx australis mantelli - Brown Kiwi # http://www.ncbi.nlm.nih.gov/Traces/wgs/?val=JYOU01 # the description page is missing from the genbank directory # there is no chrMt sequence in this release or in NCBI nucleotide ############################################################################# # fetch sequence from new style download directory (Done - 2015-12-10 Chris ) # NCBI has redesigned their FTP download site, new type of address # and naming scheme mkdir -p /hive/data/genomes/aptMan1/refseq cd /hive/data/genomes/aptMan1/refseq time rsync -L -a -P \ rsync://ftp.ncbi.nlm.nih.gov/genomes/refseq/vertebrate_other/Apteryx_australis/all_assembly_versions/GCF_001039765.1_AptMant0/ ./ # real 1m12.690s # measure what we have here: faSize GCF_001039765.1_AptMant0_genomic.fna.gz #1523972539 bases (212971491 N's 1311001048 real 1093095933 upper 217905115 lower) in 24720 sequences in 1 files #Total size: mean 61649.4 sd 839460.1 min 1000 (NW_014006041.1) max 63182071 (NW_013995860.1) median 1776 #N count: mean 8615.4 sd 64628.4 #U count: mean 44219.1 sd 637623.2 #L count: mean 8814.9 sd 140154.0 #%14.30 masked total, %16.62 masked real ############################################################################# # fixup to UCSC naming scheme (Done - 2015-09-15 - Chris) mkdir /hive/data/genomes/aptMan1/ucsc cd /hive/data/genomes/aptMan1/ucsc # since this is a scaffold-only assembly, merely use the accession names # and since there are all .1 versions, this sed statement will make them # all v1 version names: zcat ../refseq/*assembly_structure/Primary_Assembly/unplaced_scaffolds/AGP/unplaced.scaf.agp.gz \ | grep -v "^#" | sed -e 's/\.1/v1/;' > chrUn.aptMan1.agp time zcat ../refseq/*assembly_structure/Primary_Assembly/unplaced_scaffolds/FASTA/unplaced.scaf.fna.gz \ | sed -e 's/.1 Apteryx .*/v1/;' > chrUn.aptMan1.fa # verify these two files are compatible: faToTwoBit chrUn.aptMan1.fa test.2bit time checkAgpAndFa chrUn.aptMan1.agp test.2bit 2>&1 | tail # All AGP and FASTA entries agree - both files are valid rm test.2bit # fetch photo: mkdir /hive/data/genomes/aptMan1/photo cd /hive/data/genomes/aptMan1/photo wget --timestamping \ http://www.md.ucl.ac.be/peca/test/Brown%20Kiwi.jpg # The file was cropped using mac default cropping (cmd+shift+4) convert -quality 80 -geometry "400x300" brownKiwi.jpg \ bk.jpg # check that into the source tree hg/htdocs/images/ cp bk.jpg /cluster/home/ceisenhart/kent/src/hg/htdocs/images/Apteryx_australis.jpg cd /cluster/home/ceisenhart/kent/src/hg/htdocs/images/ git add Apteryx_australis.jpg # add in the link next time! git commit -m "photo courtesy of S. Moniotte, refs #16029" # and copy over to /usr/local/apache/htdocs/images/Nanorana_parkeri.jpg # permission obtained: ############################################################################# # Initial database build (Done - 2015-12-10 Chris) cd /hive/data/genomes/aptMan1 printf "%s" '# Config parameters for makeGenomeDb.pl: db aptMan1 clade vertebrate genomeCladePriority 50 # Seems to serve no purpose... scientificName Apteryx australis mantelli commonName Brown kiwi assemblyDate Jun. 2015 assemblyLabel Max-Plank Institute for Evolutionary Anthropology AptMant0 assemblyShortLabel MPI-EVA AptMant0 orderKey 2715 mitoAcc LK054805.1 fastaFiles /hive/data/genomes/aptMan1/ucsc/*.fa agpFiles /hive/data/genomes/aptMan1/ucsc/*.agp # qualFiles none dbDbSpeciesDir birds photoCreditURL http://www.md.ucl.ac.be/peca/test/copyright.html photoCreditName S. Moniotte ncbiGenomeId 10907 ncbiAssemblyId 356101 ncbiAssemblyName AptMant0 ncbiBioProject 287231 genBankAccessionID GCA_001039765.1 taxId 202946 ' > aptMan1.config.ra # verify sequence and AGP are OK: time (makeGenomeDb.pl -workhorse=hgwdev -dbHost=hgwdev -fileServer=hgwdev \ -stop=agp aptMan1.config.ra) > agp.log 2>&1 # *** All done! (through the 'agp' step) # real 1m35.746s # then finish it off: time (makeGenomeDb.pl -workhorse=hgwdev -dbHost=hgwdev \ -fileServer=hgwdev -continue=db aptMan1.config.ra) > db.log 2>&1 time (makeGenomeDb.pl -workhorse=hgwdev -dbHost=hgwdev \ -fileServer=hgwdev -continue=trackDb aptMan1.config.ra) > trackDb.log 2>&1 # real 15m49.649s # check in the trackDb files created and add to trackDb/makefile ############################################################################## # cpgIslands on UNMASKED sequence (DONE - 2015-12-10 - Chris) mkdir /hive/data/genomes/aptMan1/bed/cpgIslandsUnmasked cd /hive/data/genomes/aptMan1/bed/cpgIslandsUnmasked time (doCpgIslands.pl -dbHost=hgwdev -bigClusterHub=ku -buildDir=`pwd` \ -tableName=cpgIslandExtUnmasked \ -maskedSeq=/hive/data/genomes/aptMan1/aptMan1.unmasked.2bit \ -workhorse=hgwdev -smallClusterHub=ku aptMan1) > do.log 2>&1 cat fb.aptMan1.cpgIslandExtUnmasked.txt #36538307 bases of 1311306859 (2.786%) in intersection ############################################################################# # cytoBandIdeo - (DONE - 2015-12-10 - Chris) mkdir /hive/data/genomes/aptMan1/bed/cytoBand cd /hive/data/genomes/aptMan1/bed/cytoBand makeCytoBandIdeo.csh aptMan1 ######################################################################### # ucscToINSDC table/track (TBD - 2015-03-20 - Hiram) mkdir /hive/data/genomes/aptMan1/bed/ucscToINSDC cd /hive/data/genomes/aptMan1/bed/ucscToINSDC ~/kent/src/hg/utils/automation/ucscToINSDC.sh \ ../../genbank/GCA_*assembly_structure/Primary_Assembly 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 * # 25187 name.coordinate.tab # 25187 ucscToINSDC.bed # 25187 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/" $HOME/kent/src/hg/lib/ucscToINSDC.sql \ | hgLoadSqlTab aptMan1 ucscToINSDC stdin ucscToINSDC.bed checkTableCoords aptMan1 # should cover %100 entirely: featureBits -countGaps aptMan1 ucscToINSDC # 2053849526 bases of 2053849526 (100.000%) in intersection ######################################################################### # fixup search rule for assembly track/gold table (TBD - 2015-03-20 - Hiram) hgsql -N -e "select frag from gold;" aptMan1 | sort | head -1 JYOU01000001.1 hgsql -N -e "select frag from gold;" aptMan1 | sort | tail -2 JYOU01147511.1 JYOU01147512.1 # verify this rule will find them all or eliminate them all: hgsql -N -e "select frag from gold;" aptMan1 | wc -l # 147512 hgsql -N -e "select frag from gold;" aptMan1 \ | egrep -e 'JYOU01[0-9]+(\.1)?' | wc -l # 147512 hgsql -N -e "select frag from gold;" aptMan1 \ | egrep -v -e 'JYOU01[0-9]+(\.1)?' | wc -l # 0 # hence, add to trackDb/tarsier/aptMan1/trackDb.ra searchTable gold shortCircuit 1 termRegex JYOU01[0-9]+(\.1)? query select chrom,chromStart,chromEnd,frag from %s where frag like '%s%%' searchPriority 8 ########################################################################## # running repeat masker ( DONE - 2015-12-10 - Chris) mkdir /hive/data/genomes/aptMan1/bed/repeatMasker cd /hive/data/genomes/aptMan1/bed/repeatMasker time (doRepeatMasker.pl -buildDir=`pwd` \ -bigClusterHub=ku -dbHost=hgwdev -workhorse=hgwdev \ -smallClusterHub=ku aptMan1) > do.log 2>&1 # real 232m59.124s cat faSize.rmsk.txt #1523986457 bases (212971113 N's 1311015344 real 1252680878 upper 58334466 #lower) in 24719 sequences in 1 files #Total size: mean 61652.4 sd 839476.9 min 1000 (NW_014006041v1) max #63182071 (NW_013995860v1) median 1777 #N count: mean 8615.7 sd 64629.7 #U count: mean 50676.8 sd 739119.8 #L count: mean 2359.9 sd 39090.5 #%3.83 masked total, %4.45 masked real egrep -i "versi|relea" do.log #RepeatMasker version open-4.0.5 #grep version of RepeatMasker$ /scratch/data/RepeatMasker/RepeatMasker ## January 31 2015 (open-4-0-5) version of RepeatMasker #grep RELEASE /scratch/data/RepeatMasker/Libraries/RepeatMaskerLib.embl #CC RELEASE 20140131; time featureBits -countGaps aptMan1 rmsk #58406940 bases of 1523986457 (3.833%) in intersection # #real 0m12.775s #user 0m3.215s #sys 0m0.318s ########################################################################## # running simple repeat (DONE - 2015-12-10 - Chris) mkdir /hive/data/genomes/aptMan1/bed/simpleRepeat cd /hive/data/genomes/aptMan1/bed/simpleRepeat time (doSimpleRepeat.pl -buildDir=`pwd` -bigClusterHub=ku \ -dbHost=hgwdev -workhorse=hgwdev -smallClusterHub=ku \ aptMan1) > do.log 2>&1 # real 20m20.609s cat fb.simpleRepeat # 112091725 bases of 1311306859 (8.548%) in intersection # using the Window Masker result: cd /hive/data/genomes/aptMan1 twoBitMask bed/windowMasker/aptMan1.cleanWMSdust.2bit \ -add bed/simpleRepeat/trfMask.bed aptMan1.2bit # you can safely ignore the warning about fields >= 13 twoBitToFa aptMan1.2bit stdout | faSize stdin > faSize.aptMan1.2bit.txt cat faSize.aptMan1.2bit.txt #1523986457 bases (212971113 N's 1311015344 real 1087217052 upper #223798292 lower) in 24719 sequences in 1 files #Total size: mean 61652.4 sd 839476.9 min 1000 (NW_014006041v1) max #63182071 (NW_013995860v1) median 1777 #N count: mean 8615.7 sd 64629.7 #U count: mean 43983.1 sd 634950.8 #L count: mean 9053.7 sd 142837.6 #%14.69 masked total, %17.07 masked real rm /gbdb/aptMan1/aptMan1.2bit ln -s `pwd`/aptMan1.2bit /gbdb/aptMan1/aptMan1.2bit ########################################################################## # CREATE MICROSAT TRACK (DONE - 2016-02-4 - Chris ) ssh hgwdev mkdir /cluster/data/aptMan1/bed/microsat cd /cluster/data/aptMan1/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 aptMan1 microsat microsat.bed # Read 4041 elements of size 4 from microsat.bed ########################################################################## ## WINDOWMASKER (DONE - 2015-12-10 - Chris) mkdir /hive/data/genomes/aptMan1/bed/windowMasker cd /hive/data/genomes/aptMan1/bed/windowMasker time (doWindowMasker.pl -buildDir=`pwd` -workhorse=hgwdev \ -dbHost=hgwdev aptMan1) > do.log 2>&1 # real 153m54.144s # Masking statistics cat faSize.aptMan1.cleanWMSdust.txti #1523986457 bases (212971113 N's 1311015344 real 1087495173 upper #223520171 lower) in 24719 sequences in 1 files #Total size: mean 61652.4 sd 839476.9 min 1000 (NW_014006041v1) max #63182071 (NW_013995860v1) median 1777 #N count: mean 8615.7 sd 64629.7 #U count: mean 43994.3 sd 635058.8 #L count: mean 9042.4 sd 142728.8 #%14.67 masked total, %17.05 masked real cat fb.aptMan1.rmsk.windowmaskerSdust.txt #28675883 bases of 1523986457 (1.882%) in intersection ########################################################################## # cpgIslands - (DONE - 2015-12-10 - Chris) mkdir /hive/data/genomes/aptMan1/bed/cpgIslands cd /hive/data/genomes/aptMan1/bed/cpgIslands time (doCpgIslands.pl -dbHost=hgwdev -bigClusterHub=ku \ -workhorse=hgwdev -smallClusterHub=ku aptMan1) > do.log 2>&1 & # real 117m34.561s # failed during kluster hardMask operation, continuing: time (doCpgIslands.pl -dbHost=hgwdev -bigClusterHub=ku \ -continue=cpg -workhorse=hgwdev -smallClusterHub=ku aptMan1) \ > cpg.log 2>&1 & # real 10m28.915s cat fb.aptMan1.cpgIslandExt.txt # 31431262 bases of 1311306859 (2.397%) in intersection ######################################################################### # genscan - (Done - 2015-12-11 - Chris) mkdir /hive/data/genomes/aptMan1/bed/genscan cd /hive/data/genomes/aptMan1/bed/genscan time (doGenscan.pl -buildDir=`pwd` -workhorse=hgwdev -dbHost=hgwdev \ -bigClusterHub=ku aptMan1) > do.log 2>&1 # real 57m21.101s cat fb.aptMan1.genscan.txt # 55630505 bases of 1977771384 (2.813%) in intersection cat fb.aptMan1.genscanSubopt.txt # 58340692 bases of 1977771384 (2.950%) in intersection ############################################################################# # generic example procedure: mkdir /hive/data/genomes/aptMan1/bed/augustus cd /hive/data/genomes/aptMan1/bed/augustus time (doAugustus.pl -buildDir=`pwd` -bigClusterHub=ku \ -species=chicken -dbHost=hgwdev \ -workhorse=hgwdev aptMan1) > do.log 2>&1 # real 112m36.188s # user 0m0.489s # sys 0m0.729 cat fb.aptMan1.augustusGene.txt #24772963 bases of 1311306859 (1.889%) in intersection ######################################################################## # Create kluster run files (Done - 2015-12-22 - Chris) cd /hive/data/genomes/aptMan1 # numerator is aptMan1 gapless bases "real" as reported by: head -1 faSize.aptMan1.2bit.txt #1523986457 bases (212971113 N's 1311015344 real 1087217052 upper #223798292 lower) in 24719 sequences in 1 files # numerator is 'real' base count # denominator is hg19 gapless bases as reported by: # featureBits -noRandom -noHap hg19 gap # 1024 is threshold used for human -repMatch: calc \( 1311015344 / 2861349177 \) \* 1024 # ( 1311015344 / 2861349177 ) * 1024 = 469.177171 # ==> use -repMatch=700 according to size scaled down from 1024 for human. # and rounded down to nearest 50 cd /hive/data/genomes/aptMan1 time blat aptMan1.2bit \ /dev/null /dev/null -tileSize=11 -makeOoc=jkStuff/aptMan1.11.ooc \ -repMatch=400 # Wrote 21445 overused 11-mers to jkStuff/aptMan1.11.ooc # Done making jkStuff/aptMan1.11.ooc # # real 0m27.556s # user 0m26.401s # sys 0m1.033s # 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;' aptMan1 \ | ave -tableOut -col=7 stdin # There are no non-bridged gaps # # 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 aptMan1 jkStuff/aptMan1.nonBridged.lft \ # -bedFile=jkStuff/aptMan1.nonBridged.bed # hgsql -N \ # -e 'select * from gap where bridge="no" order by size;' aptMan1 \ # | ave -col=7 stdin # not needed: # gapToLift -verbose=2 -minGap=100 bosTau7 jkStuff/nonBridged.lft \ # -bedFile=jkStuff/nonBridged.bed ## reading: chrom.sizes ## contig count: 24719, total size: 1523986457, one half size: 761993228 ## cumulative N50 count contig contig size #757321977 50 NW_013989770v1 5713742 #761993228 one half size #763000997 51 NW_014004284v1 5679020 ############################################################################# # GENBANK AUTO UPDATE (DONE - 2015-12-22 - Chris) ssh hgwdev cd $HOME/kent/src/hg/makeDb/genbank git pull # /cluster/data/genbank/data/organism.lst shows: # #organism mrnaCnt estCnt refSeqCnt # Apteryx australis australis 1 0 0 # Apteryx australis mantelli 1 0 1 # Apteryx owenii 5 0 0 # edit etc/genbank.conf to add aptMan1 just before xenTro7 # aptMan1 (brown kiwi) aptMan1.serverGenome = /hive/data/genomes/aptMan1/aptMan1.2bit aptMan1.clusterGenome = /hive/data/genomes/aptMan1/aptMan1.2bit aptMan1.ooc = /hive/data/genomes/aptMan1/jkStuff/aptMan1.11.ooc aptMan1.lift = no aptMan1.perChromTables = no aptMan1.refseq.mrna.xeno.pslCDnaFilter = ${lowCover.refseq.mrna.xeno.pslCDnaFilter} aptMan1.refseq.mrna.native.pslCDnaFilter = ${lowCover.refseq.mrna.native.pslCDnaFilter} aptMan1.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter} aptMan1.genbank.mrna.xeno.pslCDnaFilter = ${lowCover.genbank.mrna.xeno.pslCDnaFilter} aptMan1.genbank.est.native.pslCDnaFilter = ${lowCover.genbank.est.native.pslCDnaFilter} aptMan1.genbank.est.xeno.pslCDnaFilter = ${lowCover.genbank.est.xeno.pslCDnaFilter} aptMan1.downloadDir = aptMan1 # Edit src/lib/gbGenome.c to add new species. git commit -m "Added aptMan brown kiwi refs #16029" \ etc/genbank.conf src/lib/gbGenome.c git push # update /cluster/data/genbank/etc/: make etc-update # update /cluster/data/genbank/bin/: # Hiram manually changed the compiler settings to get this through # (HG-WARN) make install-server screen # control this business with a screen since it takes a while cd /cluster/data/genbank time ./bin/gbAlignStep -initial aptMan1 # #real 249m59.353s #user 37m10.703s #sys 192m17.108s # logFile: var/build/logs/2015.12.21-10:29:28.aptMan1.initalign.log # To re-do, rm the dir first: # /cluster/data/genbank/work/initial.aptMan1 # load database when finished ssh hgwdev cd /cluster/data/genbank time ./bin/gbDbLoadStep -drop -initialLoad aptMan1 #logFile: var/dbload/hgwdev/logs/2015.12.22-10:50:30.aptMan1.dbload.log # #real 84m57.390s #user 12m35.070s #sys 68m18.331s # enable daily alignment and update of hgwdev cd ~/kent/src/hg/makeDb/genbank git pull # add aptMan1 to: # vi etc/align.dbs etc/hgwdev.dbs git commit -m "Added aptMan1 - Brown Kiwi refs #16029" etc/align.dbs etc/hgwdev.dbs git push make etc-update ######################################################################### # all.joiner update, downloads and in pushQ - (Done - 2016-01-06 - Chris) cd $HOME/kent/src/hg/makeDb/schema # fixup all.joiner until this is a clean output joinerCheck -database=aptMan1 -tableCoverage all.joiner joinerCheck -database=aptMan1 -times all.joiner joinerCheck -database=aptMan1 -keys all.joiner cd /hive/data/genomes/aptMan1 time makeDownloads.pl aptMan1 > downloads.log 2>&1i # #real 10m45.282s #user 0m0.690s #sys 0m0.500s # now ready for pushQ entry mkdir /hive/data/genomes/aptMan1/pushQ cd /hive/data/genomes/aptMan1/pushQ makePushQSql.pl aptMan1 > aptMan1.pushQ.sql 2> stderr.out # check for errors in stderr.out, some are OK, e.g.: # WARNING: hgwdev does not have /gbdb/aptMan1/wib/gc5Base.wib cd /hive/data/genomes/aptMan1/pushQ makePushQSql.pl aptMan1 > aptMan1.pushQ.sql 2> stderr.out # check for errors in stderr.out, some are OK, e.g.: #WARNING: hgwdev does not have /gbdb/aptMan1/wib/gc5Base.wib #WARNING: hgwdev does not have /gbdb/aptMan1/wib/quality.wib #WARNING: hgwdev does not have /gbdb/aptMan1/bbi/qualityBw/quality.bw #WARNING: aptMan1 does not have seq #WARNING: aptMan1 does not have extFile #WARNING: aptMan1 does not have estOrientInfo # copy it to hgwbeta scp -p aptMan1.pushQ.sql qateam@hgwbeta:/tmp ssh qateam@hgwbeta "./bin/x86_64/hgsql qapushq < /tmp/aptMan1.pushQ.sql" # in that pushQ entry walk through each entry and see if the # sizes will set properly #########################################################################