# for emacs: -*- mode: sh; -*- # DATE: 31-May-2012 # ORGANISM: Alligator mississippiensis # TAXID: 8496 # ASSEMBLY LONG NAME: allMis0.2 # ASSEMBLY SHORT NAME: allMis0.2 # ASSEMBLY SUBMITTER: International Crocodilian Genomes Working Group # ASSEMBLY TYPE: Haploid # NUMBER OF ASSEMBLY-UNITS: 1 # ASSEMBLY ACCESSION: GCA_000281125.1 # FTP-RELEASE DATE: 07-Aug-2012 # http://www.ncbi.nlm.nih.gov/genome/13409 # http://www.ncbi.nlm.nih.gov/assembly/406428/ # http://www.ncbi.nlm.nih.gov/bioproject/159843 # http://www.ncbi.nlm.nih.gov/Traces/wgs/?val=AKHW01 # Genome Coverage : 68x # http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=8496 # rsync://ftp.ncbi.nlm.nih.gov/genbank/genomes/Eukaryotes/vertebrates_other/Alligator_mississippiensis/allMis0.2/ ########################################################################## # Download sequence (DONE - 2012-08-23 - Hiram) mkdir /hive/data/genomes/allMis1 cd /hive/data/genomes/allMis1 mkdir genbank cd genbank rsync -a -P \ rsync://ftp.ncbi.nlm.nih.gov/genbank/genomes/Eukaryotes/vertebrates_other/Alligator_mississippiensis/allMis0.2/ ./ # verify the size of the sequence here: faSize Primary_Assembly/unplaced_scaffolds/FASTA/unplaced.scaf.fa.gz # 2174243242 bases (45539765 N's 2128703477 real 2128703477 upper 0 lower) # in 14644 sequences in 1 files # Total size: mean 148473.3 sd 283025.3 min 816 (gi|397224103|gb|AKHW01085896.1|) # max 4958242 (gi|397457027|gb|JH738473.1|) median 25764 # %0.00 masked total, %0.00 masked real # strip the names down to something reasonable, they can all be: # >JH7[0-9] zcat Primary_Assembly/unplaced_scaffolds/FASTA/unplaced.scaf.fa.gz \ | sed -e "s/^>.*JH7/>JH7/; s/^>.*AKHW01/>AKHW01/; s/.1. Alligator.*//" \ | gzip -c > ucsc.fa.gz zcat Primary_Assembly/unplaced_scaffolds/AGP/unplaced.scaf.agp.gz \ | sed -e "s/^\(JH7[0-9]*\).1/\1/; s/^\(AKHW01[0-9]*\).1/\1/;" \ | gzip -c > ucsc.agp.gz time checkAgpAndFa ucsc.agp.gz ucsc.fa.gz 2>&1 | tail -2 # Valid Fasta file entry # All AGP and FASTA entries agree - both files are valid # real 0m59.548s mkdir /hive/data/genomes/allMis1/photograph cd /hive/data/genomes/allMis1/photograph wget --timestamping \ http://www.nasa.gov/centers/kennedy/images/content/91159main_93pc780.jpg convert -geometry "220x300" 91159main_93pc780.jpg \ Alligator_Mississippiensis.jpg # check this .jpg file into the source tree kent/src/hg/htdocs/images/ git commit -m "gator photo from NASA Kennedy" Alligator_Mississippiensis.jpg # and copy to /usr/local/apache/htdocs/images cp -p Alligator_Mississippiensis.jpg /usr/local/apache/htdocs/images ########################################################################## # Initial makeGenomeDb.pl (DONE - 2012-08-23 - Hiram) # obtain a template for this from the source tree: # kent/src/hg/utils/automation/configFiles/ # and check it back into the source tree when completed here: cd /hive/data/genomes/geoFor1 cat << '_EOF_' > geoFor1.config.ra # Config parameters for makeGenomeDb.pl: db allMis1 clade vertebrate genomeCladePriority 68 scientificName Alligator Mississippiensis commonName American alligator assemblyDate Aug. 2012 assemblyLabel International Crocodilian Genomes Working Group assemblyShortLabel allMis0.2 orderKey 4380 mitoAcc NC_001922 fastaFiles /hive/data/genomes/allMis1/genbank/ucsc.fa.gz agpFiles /hive/data/genomes/allMis1/genbank/ucsc.agp.gz # qualFiles none dbDbSpeciesDir gator photoCreditURL http://green.soe.ucsc.edu/ photoCreditName Photo courtesy of the Green Lab, U.C. Santa Cruz ncbiGenomeId 13409 ncbiAssemblyId 406428 ncbiAssemblyName allMis0.2 ncbiBioProject 159843 genBankAccessionID GCA_000281125.1 taxId 8496 '_EOF_' # << happy emacs time makeGenomeDb.pl -workhorse=hgwdev -fileServer=hgwdev -dbHost=hgwdev \ -stop=agp allMis1.config.ra > agp.log 2>&1 # real 2m32.247s # verify OK: tail -1 agp.log # *** All done! (through the 'agp' step) # finish it off time makeGenomeDb.pl -continue=db -workhorse=hgwdev -fileServer=hgwdev \ -dbHost=hgwdev allMis1.config.ra > db.log 2>&1 # real 16m30.326s # was missing the photograph, it needs to exist for this to complete: time makeGenomeDb.pl -continue=trackDb -workhorse=hgwdev \ -fileServer=hgwdev -dbHost=hgwdev allMis1.config.ra > trackDb.log 2>&1 # real 9m24.133s # add the trackDb entries to the source tree, and the 2bit link: ln -s `pwd`/allMis1.unmasked.2bit /gbdb/allMis1/allMis1.2bit # browser should function now hgsql -e 'update defaultDb set name="allMis1" where name="allMis9";' \ hgcentraltest ########################################################################## # running repeat masker (DONE - 2012-07-26 - Hiram) mkdir /hive/data/genomes/allMis1/bed/repeatMasker cd /hive/data/genomes/allMis1/bed/repeatMasker time doRepeatMasker.pl -buildDir=`pwd` -noSplit \ -bigClusterHub=swarm -dbHost=hgwdev -workhorse=hgwdev \ -smallClusterHub=encodek allMis1 > do.log 2>&1 & # real 50m40.986s XXX - finished ! - checking with Robert Hubley about this # try this again with special library via John St. John - David Ray time doRepeatMasker.pl -buildDir=`pwd` -noSplit \ -bigClusterHub=swarm -dbHost=hgwdev -workhorse=hgwdev \ -customLib `pwd`/aMiss.rmsk.lib.v2.fa \ -smallClusterHub=encodek allMis1 > do.log 2>&1 & # real 160m45.535s XXX - finished ! - checking with Robert Hubley about this for a newer repeat lib cat faSize.rmsk.txt # 2174259888 bases (45539765 N's 2128720123 real 1587364247 upper # 541355876 lower) in 14645 sequences in 1 files # Total size: mean 148464.3 sd 283017.8 min 816 (AKHW01085896) # max 4958242 (JH738473) median 25754 # %24.90 masked total, %25.43 masked real egrep -i "versi|relea" do.log # April 26 2011 (open-3-3-0) version of RepeatMasker # CC RELEASE 20110920; # RepeatMasker version development-$Id: RepeatMasker,v 1.26 2011/09/26 16:19:44 angie Exp $ featureBits -countGaps allMis1 rmsk # 60063362 bases of 1065292181 (5.638%) in intersection # 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 - 2012-08-28 - Hiram) mkdir /hive/data/genomes/allMis1/bed/simpleRepeat cd /hive/data/genomes/allMis1/bed/simpleRepeat time doSimpleRepeat.pl -buildDir=`pwd` -bigClusterHub=swarm \ -dbHost=hgwdev -workhorse=hgwdev -smallClusterHub=encodek \ allMis1 > do.log 2>&1 & # real 9m46.133s cat fb.simpleRepeat # 22565360 bases of 2129659933 (1.060%) in intersection ######################################################################### # Verify all gaps are marked, add any N's not in gap as type 'other' # (DONE - 2012-07-26 - Hiram) mkdir /hive/data/genomes/allMis1/bed/gap cd /hive/data/genomes/allMis1/bed/gap time nice -n +19 findMotif -motif=gattaca -verbose=4 \ -strand=+ ../../allMis1.unmasked.2bit > findMotif.txt 2>&1 # real 0m29.584s grep "^#GAP " findMotif.txt | sed -e "s/^#GAP //" > allGaps.bed time featureBits allMis1 -not gap -bed=notGap.bed # 2129659933 bases of 2129659933 (100.000%) in intersection # real 0m16.373s # can see now if allGaps.bed actually is all the gaps: hgsql -N -e "select size from gap;" allMis1 | ave stdin | grep total # total 44599955.000000 ave -col=5 allGaps.bed | grep total # total 45539765.000000 # not the same count, not all gaps are marked time featureBits allMis1 allGaps.bed notGap.bed -bed=new.gaps.bed # 939810 bases of 2129659933 (0.044%) in intersection # real 44m59.537s XXX - ready to continue this # check if any non-bridged gaps here: hgsql -N -e "select bridge from gap;" allMis1 | sort | uniq -c # 68589 yes ########################################################################## ## WINDOWMASKER (DONE - 2012-07-26 - Hiram) mkdir /hive/data/genomes/allMis1/bed/windowMasker cd /hive/data/genomes/allMis1/bed/windowMasker time nice -n +19 doWindowMasker.pl -buildDir=`pwd` -workhorse=hgwdev \ -dbHost=hgwdev allMis1 > do.log 2>&1 & # real 161m54.809s XXX - ready to continue - Wed Aug 29 11:13:21 PDT 2012 # Masking statistics cat faSize.allMis1.wmsk.txt # 2174259888 bases (45539765 N's 2128720123 real 1521018315 upper # 607701808 lower) in 14645 sequences in 1 files # Total size: mean 148464.3 sd 283017.8 min 816 (AKHW01085896) # max 4958242 (JH738473) median 25754 # %27.95 masked total, %28.55 masked real cat faSize.allMis1.wmsk.sdust.txt # 2174259888 bases (45539765 N's 2128720123 real 1508788037 # upper 619932086 lower) in 14645 sequences in 1 files # Total size: mean 148464.3 sd 283017.8 min 816 (AKHW01085896) # max 4958242 (JH738473) median 25754 # %28.51 masked total, %29.12 masked real cat faSize.allMis1.cleanWMSdust.txt # 2174259888 bases (45539765 N's 2128720123 real 1508788037 # upper 619932086 lower) in 14645 sequences in 1 files # Total size: mean 148464.3 sd 283017.8 min 816 (AKHW01085896) # max 4958242 (JH738473) median 25754 # %28.51 masked total, %29.12 masked real cat fb.allMis1.windowmaskerSdust.clean.txt # 619953052 bases of 2174259888 (28.513%) in intersection # how much does this window masker and repeat masker overlap: # can be done after rmsk is done XXX - waiting for RM to finish - Wed Aug 29 11:20:00 PDT 2012 featureBits -countGaps allMis1 rmsk windowmaskerSdust # 32967187 bases of 1065292181 (3.095%) in intersection ########################################################################## # add simpleRepeats to WindowMasker result (DONE - 2012-07-26 - Hiram) # add to rmsk after it is done: cd /hive/data/genomes/allMis1 twoBitMask -add bed/windowMasker/allMis1.cleanWMSdust.2bit \ bed/simpleRepeat/trfMask.bed allMis1.2bit # you can safely ignore the warning about fields >= 13 twoBitToFa allMis1.2bit stdout | faSize stdin > faSize.allMis1.2bit.txt cat faSize.allMis1.2bit.txt # 1065292181 bases (24006152 N's 1041286029 real 833083628 upper # 208202401 lower) in 27239 sequences in 1 files # Total size: mean 39109.1 sd 545732.4 min 131 (JH767125) # max 30495534 (JH739887) median 598 # %19.54 masked total, %19.99 masked real rm /gbdb/allMis1/allMis1.2bit ln -s `pwd`/allMis1.2bit /gbdb/allMis1/allMis1.2bit ########################################################################## # cpgIslands - (DONE - 2012-07-26 - Hiram) mkdir /hive/data/genomes/allMis1/bed/cpgIslands cd /hive/data/genomes/allMis1/bed/cpgIslands time doCpgIslands.pl allMis1 > do.log 2>&1 # real 17m6.876s cat fb.allMis1.cpgIslandExt.txt # 5087816 bases of 1041286029 (0.489%) in intersection ######################################################################### # genscan - (DONE - 2012-07-26 - Hiram) mkdir /hive/data/genomes/allMis1/bed/genscan cd /hive/data/genomes/allMis1/bed/genscan time doGenscan.pl allMis1 > do.log 2>&1 # real 31m32.788s # Completed: 27239 of 27239 jobs # CPU time in finished jobs: 28s 0.47m 0.01h 0.00d 0.000 y # IO & Wait Time: 96830s 1613.83m 26.90h 1.12d 0.003 y # Average job time: 4s 0.06m 0.00h 0.00d # Longest finished job: 16s 0.27m 0.00h 0.00d # Submission to last job: 154s 2.57m 0.04h 0.00d # Estimated complete: 0s 0.00m 0.00h 0.00d cat fb.allMis1.genscan.txt # 18118133 bases of 1041286029 (1.740%) in intersection cat fb.allMis1.genscanSubopt.txt # 22582067 bases of 1041286029 (2.169%) in intersection ######################################################################### # MAKE 11.OOC FILE FOR BLAT/GENBANK (DONE - 2012-07-26 - Hiram) # Use -repMatch=400, based on size -- for human we use 1024 # use the "real" number from the faSize measurement, # hg19 is 2897316137, calculate the ratio factor for 1024: calc \( 1041286029 / 2897316137 \) \* 1024 # ( 1041286029 / 2897316137 ) * 1024 = 368.022281 # round up to 400 (melUnd1 was also 400) cd /hive/data/genomes/allMis1 time blat allMis1.2bit /dev/null /dev/null -tileSize=11 \ -makeOoc=jkStuff/allMis1.11.ooc -repMatch=400 # Wrote 14450 overused 11-mers to jkStuff/allMis1.11.ooc # real 0m32.689s # melUnd1 was: Wrote 14287 overused 11-mers to jkStuff/melUnd1.11.ooc # there are no non-bridged gaps, no lift file needed for genbank hgsql -N -e "select bridge from gap;" allMis1 | sort | uniq -c # 68589 yes # cd /hive/data/genomes/allMis1/jkStuff # gapToLift allMis1 allMis1.nonBridged.lift -bedFile=allMis1.nonBridged.bed # largest non-bridged contig: # awk '{print $3-$2,$0}' allMis1.nonBridged.bed | sort -nr | head # 123773608 chrX 95534 123869142 chrX.01 ######################################################################### # AUTO UPDATE GENBANK (DONE - 2012-07-26 - Hiram) # examine the file: /cluster/data/genbank/data/organism.lst # for your species to see what counts it has for: # organism mrnaCnt estCnt refSeqCnt # Geospiza fortis 1 0 0 # to decide which "native" mrna or ests you want to specify in genbank.conf ssh hgwdev cd $HOME/kent/src/hg/makeDb/genbank git pull # edit etc/genbank.conf to add allMis1 just after ce2 # allMis1 (Medium Ground Finch - Darwin finch) allMis1.serverGenome = /hive/data/genomes/allMis1/allMis1.2bit allMis1.clusterGenome = /hive/data/genomes/allMis1/allMis1.2bit allMis1.ooc = /hive/data/genomes/allMis1/jkStuff/allMis1.11.ooc allMis1.lift = no allMis1.refseq.mrna.native.pslCDnaFilter = ${lowCover.refseq.mrna.native.pslCDnaFilter} allMis1.refseq.mrna.xeno.pslCDnaFilter = ${lowCover.refseq.mrna.xeno.pslCDnaFilter} allMis1.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter} allMis1.genbank.mrna.xeno.pslCDnaFilter = ${lowCover.genbank.mrna.xeno.pslCDnaFilter} allMis1.genbank.est.native.pslCDnaFilter = ${lowCover.genbank.est.native.pslCDnaFilter} allMis1.refseq.mrna.native.load = no allMis1.refseq.mrna.xeno.load = yes allMis1.genbank.mrna.xeno.load = no allMis1.genbank.est.native.load = no allMis1.downloadDir = allMis1 allMis1.perChromTables = no # end of section added to etc/genbank.conf git commit -m "adding allMis1 medium ground finch" etc/genbank.conf git push make etc-update git pull # Edit src/lib/gbGenome.c to add new species. git commit -m "adding definition for geoForNames" src/lib/gbGenome.c git push make install-server ssh hgwdev # used to do this on "genbank" machine screen -S allMis1 # long running job managed in screen cd /cluster/data/genbank time nice -n +19 ./bin/gbAlignStep -initial allMis1 & # var/build/logs/2012.07.26-22:50:11.allMis1.initalign.log # real 175m22.294s # load database when finished ssh hgwdev cd /cluster/data/genbank time nice -n +19 ./bin/gbDbLoadStep -drop -initialLoad allMis1 & # real 9m57.487s # var/dbload/hgwdev/logs/2012.07.27-14:05:35.dbload.log # check the end of that dbload.log to see if it was successful # hgwdev 2012.07.27-14:15:33 dbload: finish # enable daily alignment and update of hgwdev (DONE - 2012-05-09 - Hiram) cd ~/kent/src/hg/makeDb/genbank git pull # add allMis1 to: vi etc/align.dbs etc/hgwdev.dbs git commit -m "Added allMis1." etc/align.dbs etc/hgwdev.dbs git push make etc-update ######################################################################### # set default position to FOXP2 gene displays (DONE - 2012-08-02 - Hiram) hgsql -e \ 'update dbDb set defaultPos="JH739914:135428-435957" where name="allMis1";' \ hgcentraltest ############################################################################ # downloads and pushQ entry (DONE - 2012-07-27 - Hiram) # after adding allMis1 to the all.joiner file and verifying that # joinerCheck is clean, can construct the downloads: cd /hive/data/genomes/allMis1 time makeDownloads.pl -workhorse=hgwdev allMis1 # real 11m40.799s mkdir /hive/data/genomes/allMis1/pushQ cd /hive/data/genomes/allMis1/pushQ # Mark says don't let the transMap track get there time makePushQSql.pl allMis1 2> stderr.txt | grep -v transMap > allMis1.sql # real 3m52.778s # check the stderr.txt for bad stuff, these kinds of warnings are OK: # WARNING: hgwdev does not have /gbdb/allMis1/wib/gc5Base.wib # WARNING: hgwdev does not have /gbdb/allMis1/wib/quality.wib # WARNING: hgwdev does not have /gbdb/allMis1/bbi/quality.bw # WARNING: allMis1 does not have seq # WARNING: allMis1 does not have extFile # WARNING: allMis1 does not have estOrientInfo scp -p allMis1.sql hgwbeta:/tmp ssh hgwbeta "hgsql qapushq < /tmp/allMis1.sql" ########################################################################## # BLATSERVERS ENTRY (DONE - 2012-08-03 - Hiram) # After getting a blat server assigned by the Blat Server Gods, ssh hgwdev hgsql -e 'INSERT INTO blatServers (db, host, port, isTrans, canPcr) \ VALUES ("allMis1", "blat4d", "17806", "1", "0"); \ INSERT INTO blatServers (db, host, port, isTrans, canPcr) \ VALUES ("allMis1", "blat4d", "17807", "0", "1");' \ hgcentraltest # test it with some sequence ############################################################################