# for emacs: -*- mode: sh; -*- # This file describes browser build for the chlSab2 # Chlorocebus sabaeus - Green monkey/Vervet # DATE: 25-Mar-2014 # ORGANISM: Chlorocebus sabaeus # TAXID: 60711 # ASSEMBLY LONG NAME: Chlorocebus_sabeus 1.1 # ASSEMBLY SHORT NAME: Chlorocebus_sabeus 1.1 # ASSEMBLY SUBMITTER: Vervet Genomics Consortium # ASSEMBLY TYPE: Haploid # NUMBER OF ASSEMBLY-UNITS: 1 # ASSEMBLY ACCESSION: GCA_000409795.2 # FTP-RELEASE DATE: 26-Mar-2014 ############################################################################# # fetch sequence from new style download directory (DONE - 2014-04-08 - Hiram) # NCBI has redesigned their FTP download site, new type of address # and naming scheme mkdir -p /hive/data/genomes/chlSab2/genbank cd /hive/data/genomes/chlSab2/genbank rsync -a -P \ rsync://ftp.ncbi.nlm.nih.gov/genbank/genomes/Eukaryotes/vertebrates_mammals/Chlorocebus_sabaeus/Chlorocebus_sabeus_1.1/ ./ # measure what we have here: faSize Primary_Assembly/assembled_chromosomes/FASTA/*.fa.gz \ Primary_Assembly/unlocalized_scaffolds/FASTA/*.unlocalized.scaf.fa.gz \ Primary_Assembly/unplaced_scaffolds/FASTA/unplaced.scaf.fa.gz # 2789639778 bases (37655314 N's 2751984464 real 2751984464 upper 0 lower) # in 2003 sequences in 61 files # Total size: mean 1392730.8 sd 11811922.4 # min 500 (gi|501607093|gb|AQIB01158973.1|) # max 139301422 (gi|597900174|gb|CM001948.2|) median 3062 # %0.00 masked total, %0.00 masked real # fetch photo from wikimedia commons user Atamari 2015-03-24 # http://commons.wikimedia.org/wiki/User:Atamari mkdir /hive/data/genomes/chlSab2/photo cd /hive/data/genomes/chlSab2/photo wget --timestamping \ http://upload.wikimedia.org/wikipedia/commons/0/08/Chlorocebus_sabaeus_0006.jpg # crop a bit of the edges: convert -quality 100 -crop 1600x1800+400+200 Chlorocebus_sabaeus_0006.jpg \ chlSab2.cropped.jpg # and size for the gateway page convert -quality 80 -geometry 300x300 chlSab2.cropped.jpg \ Chlorocebus_sabaeus.jpg ############################################################################# # fixup to UCSC naming scheme (DONE - 2014-04-08 - Hiram) mkdir /hive/data/genomes/chlSab2/ucsc cd /hive/data/genomes/chlSab2/ucsc ~/kent/src/hg/makeDb/doc/chlSab2/fetchChrM.sh ~/kent/src/hg/makeDb/doc/chlSab2/ucscCompositeAgp.pl ~/kent/src/hg/makeDb/doc/chlSab2/unplaced.pl ~/kent/src/hg/makeDb/doc/chlSab2/unlocalized.pl # verify the sequence is still here, add the chrM to the genbank sequences: faSize ../genbank/Primary_Assembly/assembled_chromosomes/FASTA/*.fa.gz \ ../genbank/Primary_Assembly/unlocalized_scaffolds/FASTA/*.unlocalized.scaf.fa.gz \ ../genbank/Primary_Assembly/unplaced_scaffolds/FASTA/unplaced.scaf.fa.gz \ chrM.fa # 2789656328 bases (37655329 N's 2752000999 real 2752000999 upper 0 lower) # in 2004 sequences in 62 files # Total size: mean 1392044.1 sd 11809013.4 # min 500 (gi|501607093|gb|AQIB01158973.1|) # max 139301422 (gi|597900174|gb|CM001948.2|) median 3069 # and everything here is the same count: faSize chr*.fa # 2789656328 bases (37655329 N's 2752000999 real 2752000999 upper 0 lower) # in 2004 sequences in 62 files # Total size: mean 1392044.1 sd 11809013.4 min 500 (chrUn_AQIB01158973v1) # max 139301422 (chr8) median 3069 ############################################################################# # Initial database build (DONE - 2014-04-10 - Hiram) cd /hive/data/genomes/chlSab2 cat << '_EOF_' > chlSab2.config.ra # Config parameters for makeGenomeDb.pl: db chlSab2 clade primate genomeCladePriority 15 scientificName Chlorocebus sabaeus commonName Green monkey assemblyDate Mar. 2014 assemblyLabel Washington University School of Medicine assemblyShortLabel Vervet/1994-021 orderKey 7779 # chrM already included mitoAcc none fastaFiles /hive/data/genomes/chlSab2/ucsc/chr*.fa agpFiles /hive/data/genomes/chlSab2/ucsc/chr*.agp # qualFiles none dbDbSpeciesDir chlorocebus photoCreditURL http://commons.wikimedia.org/wiki/User:Atamari photoCreditName Wikimedia commons user Atamari ncbiGenomeId 13136 ncbiAssemblyId 132581 ncbiAssemblyName Vervet/1994-021 ncbiBioProject 215854 genBankAccessionID GCA_000409795.2 taxId 60711 '_EOF_' # << happy emacs # this assembly was done manually in 2014, these makeGenomeDb.pl # procedures were run in debug mode 2015-03-23 just to get dbDb setup # and trackDb # verify sequence and AGP are OK: time (makeGenomeDb.pl -workhorse=hgwdev -dbHost=hgwdev -fileServer=hgwdev \ -debug -stop=agp chlSab2.config.ra) > agp.log 2>&1 # *** All done! (through the 'agp' step) # real 1m35.746s time (makeGenomeDb.pl -workhorse=hgwdev -dbHost=hgwdev -fileServer=hgwdev \ -debug -continue=db -stop=dbDb chlSab2.config.ra) > db.log 2>&1 time (makeGenomeDb.pl -workhorse=hgwdev -dbHost=hgwdev -fileServer=hgwdev \ -debug -continue=trackDb chlSab2.config.ra) > db.log 2>&1 # check in the trackDb files created and add to trackDb/makefile ############################################################################## # cpgIslands on UNMASKED sequence (DONE - 2014-04-15 - Hiram) mkdir /hive/data/genomes/chlSab2/bed/cpgIslandsUnmasked cd /hive/data/genomes/chlSab2/bed/cpgIslandsUnmasked time (doCpgIslands.pl -dbHost=hgwdev -bigClusterHub=ku -buildDir=`pwd` \ -tableName=cpgIslandExtUnmasked \ -maskedSeq=/hive/data/genomes/chlSab2/chlSab2.unmasked.2bit \ -workhorse=hgwdev -smallClusterHub=ku chlSab2) > do.log 2>&1 # real 16m17.756s cat fb.chlSab2.cpgIslandExtUnmasked.txt # 29045833 bases of 2752019208 (1.055%) in intersection ############################################################################# # cytoBandIdeo - (DONE - 2015-03-24 - Hiram) mkdir /hive/data/genomes/chlSab2/bed/cytoBand cd /hive/data/genomes/chlSab2/bed/cytoBand makeCytoBandIdeo.csh chlSab2 ######################################################################### # ucscToINSDC table/track (DONE - 2015-03-24 - Hiram) mkdir /hive/data/genomes/chlSab2/bed/ucscToINSDC cd /hive/data/genomes/chlSab2/bed/ucscToINSDC grep chrM ../../chlSab2.agp # chrM 1 16550 1 F NC_008066 1 16550 + ~/kent/src/hg/utils/automation/ucscToINSDC.sh \ ../../genbank/Primary_Assembly NC_008066.1 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 * # 2004 name.coordinate.tab # 2004 ucscToINSDC.bed # 2004 ucscToINSDC.txt cut -f1 ucscToINSDC.bed | awk '{print length($0)}' | sort -n | tail -1 # 27 # use the 27 in this sed sed -e "s/21/27/" $HOME/kent/src/hg/lib/ucscToINSDC.sql \ | hgLoadSqlTab chlSab2 ucscToINSDC stdin ucscToINSDC.bed checkTableCoords chlSab2 # should cover %100 entirely: featureBits -countGaps chlSab2 ucscToINSDC # 2789656328 bases of 2789656328 (100.000%) in intersection ######################################################################### # fixup search rule for assembly track/gold table (DONE - 2015-03-24 - Hiram) cd ~/kent/src/hg/makeDb/trackDb/chlorocebus/chlSab2 hgsql -N -e "select frag from gold;" chlSab2 | sort -u \ > /tmp/chlSab2.frag.gold.txt export maxLen=`awk '{print length($0)}' /tmp/chlSab2.frag.gold.txt | sort -rn | head -1` echo "scan to column: $maxLen" # scan to column: 14 export C=1 while [ $C -le $maxLen ]; do echo -n " $C: " awk '{ print substr($0,'$C',1) }' /tmp/chlSab2.frag.gold.txt | sort -u | xargs echo | sed -e 's/ //g' C=`echo $C | awk '{print $1+1}'` done # 1: AN # 2: CQ # 3: 2I_ # 4: 034B # 5: 012489 # 6: 0123456789 # 7: 0123456789 # 8: 0123456789 # 9: .0123456789 # 10: 0123456789 # 11: 0123456789 # 12: 0123456789 # 13: . # 14: 1 # verify this rule will find them all or eliminate them all: hgsql -N -e "select frag from gold;" chlSab2 | wc -l # 163018 hgsql -N -e "select frag from gold;" chlSab2 \ | egrep -e '[AN][CQ][BI0234_]+[0-9]+(\.[0-9][0-9]*)?' | wc -l # 163018 hgsql -N -e "select frag from gold;" chlSab2 \ | egrep -v -e '[AN][CQ][BI0234_]+[0-9]+(\.[0-9][0-9]*)?' | wc -l # 0 # hence, add to trackDb/tarsier/chlSab2/trackDb.ra searchTable gold shortCircuit 1 termRegex [AN][CQ][BI0234_]+[0-9]+(\.[0-9][0-9]*)? query select chrom,chromStart,chromEnd,frag from %s where frag like '%s%%' searchPriority 8 ########################################################################## # running repeat masker (DONE - 2014-04-10 - Hiram) mkdir /hive/data/genomes/chlSab2/bed/repeatMasker cd /hive/data/genomes/chlSab2/bed/repeatMasker time (doRepeatMasker.pl -buildDir=`pwd` \ -bigClusterHub=ku -dbHost=hgwdev -workhorse=hgwdev \ -smallClusterHub=ku chlSab2) > do.log 2>&1 cat faSize.rmsk.txt # 2789656328 bases (37655329 N's 2752000999 real 1411482871 upper # 1340518128 lower) in 2004 sequences in 1 files # Total size: mean 1392044.1 sd 11809013.4 min 500 (chrUn_AQIB01158973v1) # max 139301422 (chr8) median 3069 # %48.05 masked total, %48.71 masked real # most interesting, NCBI had %36.84 masked total, %38.26 masked real # I wonder how they did that ? egrep -i "versi|relea" do.log # RepeatMasker version open-4.0.3 # June 20 2013 (open-4-0-3) version of RepeatMasker # CC RELEASE 20130422 time featureBits -countGaps chlSab2 rmsk # 1340995312 bases of 2789656328 (48.070%) in intersection # real 0m45.135s # 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 - 2014-04-10 - Hiram) mkdir /hive/data/genomes/chlSab2/bed/simpleRepeat cd /hive/data/genomes/chlSab2/bed/simpleRepeat time (doSimpleRepeat.pl -buildDir=`pwd` -bigClusterHub=ku \ -dbHost=hgwdev -workhorse=hgwdev -smallClusterHub=ku \ chlSab2) > do.log 2>&1 # real 20m20.609s cat fb.simpleRepeat # 72003821 bases of 2752019208 (2.616%) in intersection # using the Window Masker result: cd /hive/data/genomes/chlSab2 twoBitMask bed/windowMasker/chlSab2.cleanWMSdust.2bit \ -add bed/simpleRepeat/trfMask.bed chlSab2.2bit # you can safely ignore the warning about fields >= 13 twoBitToFa chlSab2.2bit stdout | faSize stdin > faSize.chlSab2.2bit.txt cat faSize.chlSab2.2bit.txt # 2789656328 bases (37655329 N's 2752000999 real 1409876537 upper # 1342124462 lower) in 2004 sequences in 1 files # Total size: mean 1392044.1 sd 11809013.4 min 500 (chrUn_AQIB01158973v1) # max 139301422 (chr8) median 3069 # %48.11 masked total, %48.77 masked real rm /gbdb/chlSab2/chlSab2.2bit ln -s `pwd`/chlSab2.2bit /gbdb/chlSab2/chlSab2.2bit ########################################################################## # CREATE MICROSAT TRACK (DONE - 2015-06-22 - Hiram) ssh hgwdev mkdir /cluster/data/chlSab2/bed/microsat cd /cluster/data/chlSab2/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 chlSab2 microsat microsat.bed # Read 30391 elements of size 4 from microsat.bed ########################################################################## ## WINDOWMASKER (DONE - 2014-04-10 - Hiram) mkdir /hive/data/genomes/chlSab2/bed/windowMasker cd /hive/data/genomes/chlSab2/bed/windowMasker time (doWindowMasker.pl -buildDir=`pwd` -workhorse=hgwdev \ -dbHost=hgwdev chlSab2) > do.log 2>&1 # real 153m54.144s # Masking statistics cat faSize.chlSab2.cleanWMSdust.txt # 2789656328 bases (37655329 N's 2752000999 real 1758265115 upper # 993735884 lower) in 2004 sequences in 1 files # Total size: mean 1392044.1 sd 11809013.4 min 500 (chrUn_AQIB01158973v1) # max 139301422 (chr8) median 3069 # %35.62 masked total, %36.11 masked real cat fb.chlSab2.rmsk.windowmaskerSdust.txt # 754772298 bases of 2789656328 (27.056%) in intersection ########################################################################## # cpgIslands - (DONE - 2014-04-15 - Hiram) mkdir /hive/data/genomes/chlSab2/bed/cpgIslands cd /hive/data/genomes/chlSab2/bed/cpgIslands time (doCpgIslands.pl -dbHost=hgwdev -bigClusterHub=ku \ -workhorse=hgwdev -smallClusterHub=ku chlSab2) > do.log 2>&1 & # Elapsed time: 14m55s cat fb.chlSab2.cpgIslandExt.txt # 20748654 bases of 2752019208 (0.754%) in intersection ######################################################################### # genscan - (DONE - 2014-04-16 - Hiram) mkdir /hive/data/genomes/chlSab2/bed/genscan cd /hive/data/genomes/chlSab2/bed/genscan time (doGenscan.pl -buildDir=`pwd` -workhorse=hgwdev -dbHost=hgwdev \ -bigClusterHub=ku chlSab2) > do.log 2>&1 # Elapsed time: 100m0s cat fb.chlSab2.genscan.txt # 51781072 bases of 2752019208 (1.882%) in intersection cat fb.chlSab2.genscanSubopt.txt # 50823478 bases of 2752019208 (1.847%) in intersection ######################################################################## # Create kluster run files (DONE - 2015-03-24 - Hiram) cd /hive/data/genomes/chlSab2 # numerator is chlSab2 gapless bases "real" as reported by: head -1 faSize.chlSab2.2bit.txt # 2789656328 bases (37655329 N's 2752000999 real 1409876537 upper # 1342124462 lower) in 2004 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 \( 2752000999 / 2861349177 \) \* 1024 # ( 2752000999 / 2861349177 ) * 1024 = 984.867225 # ==> use -repMatch=900 according to size scaled down from 1024 for human. # and rounded down to nearest 50 cd /hive/data/genomes/chlSab2 time blat chlSab2.2bit \ /dev/null /dev/null -tileSize=11 -makeOoc=jkStuff/chlSab2.11.ooc \ -repMatch=900 # Wrote 32373 overused 11-mers to jkStuff/chlSab2.11.ooc # real 0m48.344s # check non-bridged gaps to see what the typical size is: hgsql -N -e 'select * from gap where bridge="no" order by size;' chlSab2 \ | ave -tableOut -col=7 stdin # # min Q1 median Q3 max mean N sum stddev # 1e+06 1e+06 1e+06 1e+06 1e+06 1e+06 29 2.9e+07 0 # note they are all 1,000,000 centromere gaps gapToLift -verbose=2 -minGap=1000000 chlSab2 \ jkStuff/chlSab2.nonBridged.lft -bedFile=jkStuff/chlSab2.nonBridged.bed # survey sizes: n50.pl chrom.sizes # reading: chrom.sizes # contig count: 2004, total size: 2789656328, one half size: 1394828164 # cumulative N50 count contig contig size # 1388069355 11 chr14 107702431 # 1394828164 one half size # 1489289239 12 chr22 101219884 ############################################################################# # GENBANK AUTO UPDATE (DONE - 2015-03-24 - Hiram) ssh hgwdev cd $HOME/kent/src/hg/makeDb/genbank git pull # /cluster/data/genbank/data/organism.lst shows: # #organism mrnaCnt estCnt refSeqCnt # Chlorocebus aethiops 411 1 0 # Chlorocebus aethiops vervet 1 0 0 # Chlorocebus pygerythrus 5 0 0 # Chlorocebus pygerythrus pygerythrus 1 0 0 # Chlorocebus sabaeus 97 37787 13 # Chlorocebus tantalus 13 0 0 # edit etc/genbank.conf to add chlSab2 just before rheRox1 # chlSab2 (green monkey) (2,004 scaffolds N50 101219884) chlSab2.serverGenome = /hive/data/genomes/chlSab2/chlSab2.2bit chlSab2.clusterGenome = /hive/data/genomes/chlSab2/chlSab2.2bit chlSab2.ooc = /hive/data/genomes/chlSab2/jkStuff/chlSab2.11.ooc chlSab2.lift = /hive/data/genomes/chlSab2/jkStuff/chlSab2.nonBridged.lft chlSab2.perChromTables = no chlSab2.refseq.mrna.xeno.pslCDnaFilter = ${finished.refseq.mrna.xeno.pslCDnaFilter} chlSab2.genbank.mrna.native.pslCDnaFilter = ${finished.genbank.mrna.native.pslCDnaFilter} chlSab2.genbank.mrna.xeno.pslCDnaFilter = ${finished.genbank.mrna.xeno.pslCDnaFilter} chlSab2.genbank.est.native.pslCDnaFilter = ${finished.genbank.est.native.pslCDnaFilter} chlSab2.genbank.est.xeno.pslCDnaFilter = ${finished.genbank.est.xeno.pslCDnaFilter} chlSab2.downloadDir = chlSab2 chlSab2.refseq.mrna.native.load = no chlSab2.refseq.mrna.xeno.load = yes chlSab2.refseq.mrna.xeno.loadDesc = yes chlSab2.genbank.mrna.native.load = yes chlSab2.genbank.mrna.native.loadDesc = no chlSab2.genbank.mrna.xeno.load = yes chlSab2.genbank.mrna.xeno.loadDesc = yes chlSab2.genbank.est.native.load = yes chlSab2.genbank.est.native.loadDesc = yes # chlSab2.upstreamGeneTbl = ensGene # Edit src/lib/gbGenome.c to add new species. git commit -m "Added chlSab Chlorocebus sabaeus refs #11172" \ 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 chlSab2 # var/build/logs/2015.03.24-15:52:59.chlSab2.initalign.log # real 782m4.063s # verify it is correctly complete tail var/build/logs/2015.03.24-15:52:59.chlSab2.initalign.log # gbAlignInstall: refseq.69/chlSab2/daily.2015.0320/mrna: real=0.02 # gbAlignInstall: complete: real=3.47 # hgwdev 2015.03.25-04:39:10 chlSab2.initalign: Succeeded: chlSab2 # hgwdev 2015.03.25-04:55:03 chlSab2.initalign: finish # To re-do, rm the dir first: # /cluster/data/genbank/work/initial.chlSab2 # load database when finished ssh hgwdev cd /cluster/data/genbank time ./bin/gbDbLoadStep -drop -initialLoad chlSab2 # logFile: var/dbload/hgwdev/logs/2015.03.25-10:54:02.chlSab2.dbload.log # real 96m13.401s # there was some kind of error in loading. Brian fixed it. # enable daily alignment and update of hgwdev cd ~/kent/src/hg/makeDb/genbank git pull # add chlSab2 to: # vi etc/align.dbs etc/hgwdev.dbs git commit -m "Added chlSab Chlorocebus sabaeus refs #11173" \ etc/align.dbs etc/hgwdev.dbs git push make etc-update ######################################################################### # all.joiner update, downloads and in pushQ - (DONE - 2015-03-26 - Hiram) cd $HOME/kent/src/hg/makeDb/schema # fixup all.joiner until this is a clean output joinerCheck -database=chlSab2 -keys all.joiner joinerCheck -database=chlSab2 -tableCoverage all.joiner joinerCheck -database=chlSab2 -times all.joiner cd /hive/data/genomes/chlSab2 time makeDownloads.pl chlSab2 > downloads.log 2>&1 # real 18m25.230s # now ready for pushQ entry mkdir /hive/data/genomes/chlSab2/pushQ cd /hive/data/genomes/chlSab2/pushQ # transMap goes on its own schedule makePushQSql.pl chlSab2 2> stderr.out | grep -v transMap > chlSab2.pushQ.sql # check for errors in stderr.out, some are OK, e.g.: # WARNING: hgwdev does not have /gbdb/chlSab2/wib/gc5Base.wib # WARNING: hgwdev does not have /gbdb/chlSab2/wib/quality.wib # WARNING: hgwdev does not have /gbdb/chlSab2/bbi/qualityBw/quality.bw # WARNING: chlSab2 does not have seq # WARNING: chlSab2 does not have extFile # copy to hgwbeta and load scp -p chlSab2.pushQ.sql qateam@hgwbeta:/tmp ssh qateam@hgwbeta "./bin/x86_64/hgsql qapushq < /tmp/chlSab2.pushQ.sql" # in that pushQ entry walk through each entry and see if the # sizes will set properly ############################################################################# # augustus gene track (DONE - 2015-05-20 - Hiram) mkdir /hive/data/genomes/chlSab2/bed/augustus cd /hive/data/genomes/chlSab2/bed/augustus time (doAugustus.pl -buildDir=`pwd` -bigClusterHub=ku \ -species=human -dbHost=hgwdev -utr -workhorse=hgwdev chlSab2) \ > do.log 2>&1 # real 173m40.464s cat fb.chlSab2.augustusGene.txt # 48617795 bases of 2752019208 (1.767%) in intersection ############################################################################ # BLATSERVERS ENTRY (DONE - 2016-09-27 - 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 ("chlSab2", "blat1c", "17874", "1", "0"); \ INSERT INTO blatServers (db, host, port, isTrans, canPcr) \ VALUES ("chlSab2", "blat1c", "17875", "0", "1");' \ hgcentraltest # test it with some sequence ############################################################################ # chlSab2 - Green monkey - Ensembl Genes version 81 (DONE - 2015-08-04 - hiram) ssh hgwdev cd /hive/data/genomes/chlSab2 cat << '_EOF_' > chlSab2.ensGene.ra # required db variable db chlSab2 liftUp /hive/data/genomes/chlSab2/jkStuff/ensToUcsc.lift '_EOF_' # << happy emacs doEnsGeneUpdate.pl -ensVersion=81 chlSab2.ensGene.ra ssh hgwdev cd /hive/data/genomes/chlSab2/bed/ensGene.81 featureBits chlSab2 ensGene # 51250643 bases of 2752019208 (1.862%) in intersection *** All done! (through the 'makeDoc' step) *** Steps were performed in /hive/data/genomes/chlSab2/bed/ensGene.81 ############################################################################ ############################################################################ # chlSab2 - Green monkey - Ensembl Genes version 86 (DONE - 2016-10-18 - hiram) ssh hgwdev cd /hive/data/genomes/chlSab2 cat << '_EOF_' > chlSab2.ensGene.ra # required db variable db chlSab2 liftUp /hive/data/genomes/chlSab2/jkStuff/ensToUcsc.lift '_EOF_' # << happy emacs doEnsGeneUpdate.pl -ensVersion=86 chlSab2.ensGene.ra ssh hgwdev cd /hive/data/genomes/chlSab2/bed/ensGene.86 featureBits chlSab2 ensGene # 51250643 bases of 2752019208 (1.862%) in intersection *** All done! (through the 'makeDoc' step) *** Steps were performed in /hive/data/genomes/chlSab2/bed/ensGene.86 ############################################################################