# for emacs: -*- mode: sh; -*- # This file describes browser build for the felCat8 # cat/Felis catus -- International Cat Genome Sequencing Consortium # This is the female Abyssinian cat named Cinnamon kept by # Dr. Kristina Narfstrom at the University of Missouri ############################################################################# # fetch sequence from new style download directory (DONE - 2014-11-20 - Hiram) # NCBI has redesigned their FTP download site, new type of address # and naming scheme mkdir -p /hive/data/genomes/felCat8/genbank cd /hive/data/genomes/felCat8/genbank rsync -L -a -P \ rsync://ftp.ncbi.nlm.nih.gov/genomes/genbank/vertebrate_mammalian/Felis_catus/latest_assembly_versions/GCA_000181335.3_Felis_catus_8.0/ ./ # measure what we have here: faSize \ GCA_000181335.3_Felis_catus_8.0_assembly_structure/Primary_Assembly/assembled_chromosomes/FASTA/*.fna.gz \ GCA_000181335.3_Felis_catus_8.0_assembly_structure/Primary_Assembly/unlocalized_scaffolds/FASTA/chr*.unlocalized.scaf.fna.gz \ GCA_000181335.3_Felis_catus_8.0_assembly_structure/Primary_Assembly/unplaced_scaffolds/FASTA/unplaced.scaf.fna.gz # 2641325249 bases (41642089 N's 2599683160 real 2599683160 upper 0 lower) # in 267624 sequences in 39 files # Total size: mean 9869.5 sd 1168454.0 min 152 (AANG03201581.1) # max 240380223 (CM001378.2) median 654 # %0.00 masked total, %0.00 masked real # note that these totals do not include chrM since the GenBank ftp directory # did not include a non-nuclear directory ############################################################################# # fixup to UCSC naming scheme (DONE - 2014-11-20 - Hiram) mkdir /hive/data/genomes/felCat8/ucsc cd /hive/data/genomes/felCat8/ucsc time ~/kent/src/hg/makeDb/doc/felCat8/ucscCompositeAgp.pl \ ../genbank/GCA_000181335.3_Felis_catus_8.0_assembly_structure/Primary_Assembly # CM001393.2 E3 # CM001383.2 B3 # CM001382.2 B2 # CM001380.2 A3 # CM001386.2 C2 # CM001391.2 E1 # CM001390.2 D4 # CM001392.2 E2 # CM001385.2 C1 # CM001389.2 D3 # CM001388.2 D2 # CM001384.2 B4 # CM001395.2 F2 # CM001381.2 B1 # CM001394.2 F1 # CM001387.2 D1 # CM001378.2 A1 # CM001379.2 A2 # CM001396.2 X # real 0m32.751s time ~/kent/src/hg/makeDb/doc/felCat8/unlocalized.pl \ ../genbank/GCA_000181335.3_Felis_catus_8.0_assembly_structure/Primary_Assembly # chrD2 # chrD3 # chrA1 # chrB4 # chrA2 # chrE1 # chrC1 # chrF2 # chrB2 # chrE3 # chrC2 # chrB1 # chrX # chrD1 # chrD4 # chrA3 # chrB3 # chrE2 # chrF1 # real 0m8.317s time ~/kent/src/hg/makeDb/doc/felCat8/unplaced.pl \ ../genbank/GCA_000181335.3_Felis_catus_8.0_assembly_structure/Primary_Assembly # real 0m2.527s # verify nothing lost compared to genbank: faSize *.fa # 2641325249 bases (41642089 N's 2599683160 real 2599683160 upper 0 lower) # in 267624 sequences in 39 files # Total size: mean 9869.5 sd 1168454.0 min 152 (chrUn_AANG03201581v1) # max 240380223 (chrA1) median 654 # %0.00 masked total, %0.00 masked real # same numbers as above. ############################################################################# # Initial database build (DONE - 2014-11-20 - Hiram) cd /hive/data/genomes/felCat8 cat << '_EOF_' > felCat8.config.ra # Config parameters for makeGenomeDb.pl: db felCat8 clade mammal genomeCladePriority 17 scientificName Felis catus commonName Cat assemblyDate Nov. 2014 assemblyLabel International Cat Genome Sequencing Consortium assemblyShortLabel ICGSC Felis_catus_8.0 orderKey 2417 # chrM bioproject: 10762 mitoAcc NC_001700.1 fastaFiles /hive/data/genomes/felCat5/ucsc/*.fa agpFiles /hive/data/genomes/felCat5/ucsc/*.agp # qualFiles none dbDbSpeciesDir cat photoCreditURL http://www.genome.gov/pressDisplay.cfm?photoID=42 photoCreditName Dr. Kristina Narfstrom ncbiGenomeId 78 ncbiAssemblyId 1373248 ncbiAssemblyName Felis_catus_8.0 ncbiBioProject 16726 genBankAccessionID GCA_000181335.3 taxId 9685 '_EOF_' # << happy emacs # verify sequence and AGP are OK: time makeGenomeDb.pl -workhorse=hgwdev -dbHost=hgwdev -fileServer=hgwdev \ -stop=agp felCat8.config.ra > agp.log 2>&1 # real 3m36.748s # then finish it off: time nice -n +19 makeGenomeDb.pl -workhorse=hgwdev -dbHost=hgwdev \ -fileServer=hgwdev -continue=db felCat8.config.ra > db.log 2>&1 # real 27m30.762s # check in the trackDb files created and add to trackDb/makefile ######################################################################### # add chromAlias table (DONE - 2017-12-14 - Hiram) mkdir /hive/data/genomes/felCat8/bed/chromAlias cd /hive/data/genomes/felCat8/bed/chromAlias hgsql -N -e 'select chrom,name from ucscToRefSeq;' felCat8 \ > ucsc.refseq.tab hgsql -N -e 'select chrom,name from ucscToINSDC;' felCat8 \ | grep -v chrM > ucsc.genbank.tab printf "chrM\tU20753.1\n" >> ucsc.genbank.tab join -t$'\t' ../idKeys/felCat8.idKeys.txt \ ../../ensembl/ensemblFelCat8.idKeys.txt \ | cut -f2,3 | sort > ucsc.ensembl.tab ~/kent/src/hg/utils/automation/chromAlias.pl sort -o felCat8.chromAlias.tab felCat8.chromAlias.tab for t in refseq genbank ensembl do c0=`cat ucsc.$t.tab | wc -l` c1=`grep $t felCat8.chromAlias.tab | wc -l` ok="OK" if [ "$c0" -ne "$c1" ]; then ok="ERROR" fi printf "# checking $t: $c0 =? $c1 $ok\n" done # checking refseq: 267625 =? 267625 OK # checking genbank: 267625 =? 267625 OK # checking ensembl: 267625 =? 267625 OK hgLoadSqlTab felCat8 chromAlias ~/kent/src/hg/lib/chromAlias.sql \ felCat8.chromAlias.tab ########################################################################## # fixup search rule for assembly track/gold table (DONE - 2015-03-20 - Hiram) hgsql -N -e "select frag from gold;" felCat8 | sort | head -1 AANG03000001.1 # there are other naming patterns: hgsql -N -e "select frag from gold;" felCat8 | sort | grep -v AANG | head -2 AC145332.48 AC233257.1 hgsql -N -e "select frag from gold;" felCat8 | sort | tail -2 AY152836.1 NC_001700.1 # verify this rule will find them all or eliminate them all: hgsql -N -e "select frag from gold;" felCat8 | wc -l # 367856 hgsql -N -e "select frag from gold;" felCat8 \ | egrep -e '[AN][ACY][N0-9_][G0-9][0-9]+(\.[0-9]+)?' | wc -l # 367856 hgsql -N -e "select frag from gold;" felCat8 \ | egrep -v -e '[AN][ACY][N0-9_][G0-9][0-9]+(\.[0-9]+)?' | wc -l # 0 # hence, add to trackDb/cat/felCat8/trackDb.ra searchTable gold shortCircuit 1 termRegex [AN][ACY][N0-9_][G0-9][0-9]+(\.[0-9]+)? query select chrom,chromStart,chromEnd,frag from %s where frag like '%s%%' searchPriority 8 ########################################################################## # running repeat masker (DONE - 2014-11-21 - Hiram) mkdir /hive/data/genomes/felCat8/bed/repeatMasker cd /hive/data/genomes/felCat8/bed/repeatMasker time doRepeatMasker.pl -buildDir=`pwd` \ -bigClusterHub=ku -dbHost=hgwdev -workhorse=hgwdev \ -smallClusterHub=ku felCat8 > do.log 2>&1 # real 453m35.159s cat faSize.rmsk.txt # 2641342258 bases (41642089 N's 2599700169 real 1446287702 upper # 1153412467 lower) in 267625 sequences in 1 files # Total size: mean 9869.6 sd 1168451.9 min 152 (chrUn_AANG03201581v1) # max 240380223 (chrA1) median 654 # %43.67 masked total, %44.37 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 felCat8 rmsk # 1154358179 bases of 2641342258 (43.703%) in intersection # real 2m13.123s # 1289639153 bases of 2670044500 (48.300%) 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 2014-11-21 - Hiram) mkdir /hive/data/genomes/felCat8/bed/simpleRepeat cd /hive/data/genomes/felCat8/bed/simpleRepeat time doSimpleRepeat.pl -buildDir=`pwd` -bigClusterHub=ku \ -dbHost=hgwdev -workhorse=hgwdev -smallClusterHub=ku \ felCat8 > do.log 2>&1 # real 140m2.826s cat fb.simpleRepeat # 54549425 bases of 2599716822 (2.098%) in intersection # add to rmsk after it is done: cd /hive/data/genomes/felCat8 twoBitMask felCat8.rmsk.2bit \ -add bed/simpleRepeat/trfMask.bed felCat8.2bit # you can safely ignore the warning about fields >= 13 twoBitToFa felCat8.2bit stdout | faSize stdin > faSize.felCat8.2bit.txt cat faSize.felCat8.2bit.txt # 2641342258 bases (41642089 N's 2599700169 real 1445054690 upper # 1154645479 lower) in 267625 sequences in 1 files # Total size: mean 9869.6 sd 1168451.9 min 152 (chrUn_AANG03201581v1) # max 240380223 (chrA1) median 654 # %43.71 masked total, %44.41 masked real rm /gbdb/felCat8/felCat8.2bit ln -s `pwd`/felCat8.2bit /gbdb/felCat8/felCat8.2bit ########################################################################## # CREATE MICROSAT TRACK (DONE - 2015-06-22 - Hiram) ssh hgwdev mkdir /cluster/data/felCat8/bed/microsat cd /cluster/data/felCat8/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 felCat8 microsat microsat.bed # Read 126733 elements of size 4 from microsat.bed ########################################################################## ## WINDOWMASKER (DONE - 2014-11-21 - Hiram) mkdir /hive/data/genomes/felCat8/bed/windowMasker cd /hive/data/genomes/felCat8/bed/windowMasker time nice -n +19 doWindowMasker.pl -buildDir=`pwd` -workhorse=hgwdev \ -dbHost=hgwdev felCat8 > do.log 2>&1 # real 613m12.862s # Masking statistics cat faSize.felCat8.cleanWMSdust.txt # 2641342258 bases (41642089 N's 2599700169 real 1691420529 upper # 908279640 lower) in 267625 sequences in 1 files # Total size: mean 9869.6 sd 1168451.9 min 152 (chrUn_AANG03201581v1) # max 240380223 (chrA1) median 654 # %34.39 masked total, %34.94 masked real cat fb.felCat8.rmsk.windowmaskerSdust.txt # 649247774 bases of 2641342258 (24.580%) in intersection ########################################################################## # cpgIslands - (DONE - 2014-11-25 - Hiram) mkdir /hive/data/genomes/felCat8/bed/cpgIslands cd /hive/data/genomes/felCat8/bed/cpgIslands time doCpgIslands.pl -dbHost=hgwdev -bigClusterHub=ku \ -workhorse=hgwdev -smallClusterHub=ku felCat8 > do.log 2>&1 # real 1589m30.221s cat fb.felCat8.cpgIslandExt.txt # 44372623 bases of 2599716822 (1.707%) in intersection ############################################################################## # cpgIslands on UNMASKED sequence (DONE - 2014-11-25 - Hiram) mkdir /hive/data/genomes/felCat8/bed/cpgIslandsUnmasked cd /hive/data/genomes/felCat8/bed/cpgIslandsUnmasked # run stepwise so the loading can be done in a different table time doCpgIslands.pl -dbHost=hgwdev -bigClusterHub=ku -buildDir=`pwd` \ -tableName=cpgIslandExtUnmasked \ -maskedSeq=/hive/data/genomes/felCat8/felCat8.unmasked.2bit \ -workhorse=hgwdev -smallClusterHub=ku felCat8 > do.log 2>&1 # real 1585m9.656s cat fb.felCat8.cpgIslandExtUnmasked.txt # 69023548 bases of 2599716822 (2.655%) in intersection ############################################################################# # cytoBandIdeo - (DONE - 2015-12-02 - Hiram) mkdir /hive/data/genomes/felCat8/bed/cytoBand cd /hive/data/genomes/felCat8/bed/cytoBand makeCytoBandIdeo.csh felCat8 ######################################################################### # genscan - (DONE - 2014-11-25,12-02 - Hiram) mkdir /hive/data/genomes/felCat8/bed/genscan cd /hive/data/genomes/felCat8/bed/genscan time doGenscan.pl -buildDir=`pwd` -workhorse=hgwdev -dbHost=hgwdev \ -bigClusterHub=ku felCat8 > do.log 2>&1 # real 2252m4.489s # two jobs failed, running with reduced window size 2,000,000 # ./runGsBigLastTwo.csh chrC1 021 gtf/021/chrC1.gtf pep/021/chrC1.pep subopt/021/chrC1.bed & # ./runGsBigLastTwo.csh chrD1 028 gtf/028/chrD1.gtf pep/028/chrD1.pep subopt/028/chrD1.bed # wait # continuing time doGenscan.pl -continue=makeBed -buildDir=`pwd` -workhorse=hgwdev \ -dbHost=hgwdev -bigClusterHub=ku felCat8 > makeBed.log 2>&1 # real 14m46.164s cat fb.felCat8.genscan.txt # 60883009 bases of 2599716822 (2.342%) in intersection cat fb.felCat8.genscanSubopt.txt # 52372380 bases of 2599716822 (2.015%) in intersection ######################################################################## # Create kluster run files (DONE - 2014-12-02 - Hiram) # numerator is felCat8 gapless bases "real" as reported by: featureBits -noRandom -noHap felCat8 gap # 36037214 bases of 2383192705 (1.512%) in intersection # 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 \( 2383192705 / 2861349177 \) \* 1024 # ( 2383192705 / 2861349177 ) * 1024 = 852.880644 # ==> use -repMatch=800 according to size scaled down from 1024 for human. # and rounded down to nearest 50 cd /hive/data/genomes/felCat8 time blat felCat8.2bit \ /dev/null /dev/null -tileSize=11 -makeOoc=jkStuff/felCat8.11.ooc \ -repMatch=800 # Wrote 36446 overused 11-mers to jkStuff/felCat8.11.ooc # real 1m20.620s # check non-bridged gaps to see what the typical size is: hgsql -N -e 'select * from gap where bridge="no" order by size;' \ felCat8 | ave -col=7 stdin # Q1 100.000000 # median 100.000000 # Q3 100.000000 # average 100.000000 # min 100.000000 # max 100.000000 # count 303 # total 30300.000000 # standard deviation 0.000000 # they are all 100 bases gapToLift -verbose=2 -minGap=100 felCat8 jkStuff/felCat8.nonBridged.lft \ -bedFile=jkStuff/felCat8.nonBridged.bed cat jkStuff/felCat8.nonBridged.bed | awk '{printf "%s\t%d\n", $4,$3-$2}' \ | sort -k2nr > jkStuff/nonBridged.sizes n50.pl jkStuff/nonBridged.sizes # reading: nonBridged.sizes # contig count: 267928, total size: 2641311958, one half size: # 1320655979 # cumulative N50 count contig contig size 1307787463 44 chrC1.08 18169384 1320655979 one half size 1325860434 45 chrX.28 18072971 ######################################################################## # GENBANK AUTO UPDATE (WORKING - 2014-12-02,05 - Hiram) ssh hgwdev cd $HOME/kent/src/hg/makeDb/genbank git pull # /cluster/data/genbank/data/organism.lst shows: # #organism mrnaCnt estCnt refSeqCnt # Felis catus 2392 923 399 # edit etc/genbank.conf to add felCat8 just before felCat5 # Nov. 2014 International Cat Genome Sequencing Consortium Felis_catus_8.0 # felCat8 (Cat) felCat8.serverGenome = /hive/data/genomes/felCat8/felCat8.2bit felCat8.clusterGenome = /hive/data/genomes/felCat8/felCat8.2bit felCat8.ooc = /hive/data/genomes/felCat8/jkStuff/felCat8.11.ooc felCat8.lift = /hive/data/genomes/felCat8/jkStuff/felCat8.nonBridged.lift felCat8.perChromTables = no felCat8.refseq.mrna.native.pslCDnaFilter = ${finished.refseq.mrna.native.pslCDnaFilter} felCat8.refseq.mrna.xeno.pslCDnaFilter = ${finished.refseq.mrna.xeno.pslCDnaFilter} felCat8.genbank.mrna.native.pslCDnaFilter = ${finished.genbank.mrna.native.pslCDnaFilter} felCat8.genbank.mrna.xeno.pslCDnaFilter = ${finished.genbank.mrna.xeno.pslCDnaFilter} felCat8.genbank.est.native.pslCDnaFilter = ${finished.genbank.est.native.pslCDnaFilter} felCat8.genbank.est.xeno.pslCDnaFilter = ${finished.genbank.est.xeno.pslCDnaFilter} felCat8.genbank.mrna.xeno.load = yes felCat8.downloadDir = felCat8 felCat8.refseq.mrna.native.load = yes felCat8.refseq.mrna.xeno.load = yes felCat8.refseq.mrna.xeno.loadDesc = yes # felCat8.upstreamGeneTbl = refGene # felCat8.upstreamMaf = multiz6way # /hive/data/genomes/felCat8/bed/multiz6way/species.list git commit -m "Added felCat8; refs #14412" etc/genbank.conf git push # update /cluster/data/genbank/: make etc-update # Edit src/lib/gbGenome.c to add new species. Skipped screen # control this business with a screen since it takes a while cd /cluster/data/genbank time ./bin/gbAlignStep -initial felCat8 # logFile: var/build/logs/2014.12.02-11:51:04.felCat8.initalign.log # real 1310m38.973s # If necessary to restart from beginning, rm the dir first: # /cluster/data/genbank/work/initial.felCat8 # load database when finished ssh hgwdev cd /cluster/data/genbank time ./bin/gbDbLoadStep -drop -initialLoad felCat8 # logFile: var/dbload/hgwdev/logs/2014.12.03-21:03:57.felCat8.dbload.log # real 82m44.925s # enable daily alignment and update of hgwdev cd ~/kent/src/hg/makeDb/genbank git pull # add felCat8 to: # vi etc/align.dbs etc/hgwdev.dbs git commit -m "Added felCat8 - cat refs #14412" etc/align.dbs etc/hgwdev.dbs git push make etc-update ############################################################################ # construct liftOver to felCat5 (DONE - 2014-12-02 - Hiram) screen -S felCat5 # manage this longish running job in a screen mkdir /hive/data/genomes/felCat8/bed/blat.felCat5.2014-12-02 cd /hive/data/genomes/felCat8/bed/blat.felCat5.2014-12-02 # check it with -debug first to see if it is going to work: time doSameSpeciesLiftOver.pl -buildDir=`pwd` -bigClusterHub=ku \ -ooc=/hive/data/genomes/felCat8/jkStuff/felCat8.11.ooc \ -debug -dbHost=hgwdev -workhorse=hgwdev felCat8 felCat5 # real 0m1.838s # if that is OK, then run it: time (doSameSpeciesLiftOver.pl -buildDir=`pwd` -bigClusterHub=ku \ -ooc=/hive/data/genomes/felCat8/jkStuff/felCat8.11.ooc \ -dbHost=hgwdev -workhorse=hgwdev felCat8 felCat5) > do.log 2>&1 # real 454m20.649s # verify this file exists: # /gbdb/felCat8/liftOver/felCat8ToFelCat5.over.chain.gz # and try out the conversion on genome-test from felCat8 to felCat5 ######################################################################### # ucscToINSDC table/track (DONE - 2014-12-09 - Hiram) mkdir /hive/data/genomes/felCat8/bed/ucscToINSDC cd /hive/data/genomes/felCat8/bed/ucscToINSDC # check for chrM in assembly: grep chrM ../../felCat8.agp # chrM 1 17009 6 F NC_001700.1 1 17009 + # use the accession name from there in this command (blank if none) ~/kent/src/hg/makeDb/doc/felCat8/ucscToINSDC.sh \ ../../genbank/GCA_*assembly_structure/Primary_Assembly NC_001700.1 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 # should all be the same line count: wc -l * # 267625 name.coordinate.tab # 267625 ucscToINSDC.bed # 267625 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 felCat8 ucscToINSDC stdin ucscToINSDC.bed checkTableCoords felCat8 # should cover %100 entirely: featureBits -countGaps felCat8 ucscToINSDC # 2641342258 bases of 2641342258 (100.000%) in intersection ############################################################################ # BLATSERVERS ENTRY (DONE - 2015-03-20 - Hiram) # After getting a blat server assigned by the Blat Server Gods, ssh hgwdev # verify doesn't exist yet: hgsql -e 'select * from blatServers;' hgcentraltest | grep -i felcat # only shows felCat4 and felCat5 hgsql -e 'INSERT INTO blatServers (db, host, port, isTrans, canPcr) \ VALUES ("felCat8", "blat4d", "17856", "1", "0"); \ INSERT INTO blatServers (db, host, port, isTrans, canPcr) \ VALUES ("felCat8", "blat4d", "17857", "0", "1");' \ hgcentraltest # verify entry: hgsql -e 'select * from blatServers;' hgcentraltest | grep -i felcat # felCat8 blat4d 17856 1 0 # felCat8 blat4d 17857 0 1 # test it with some sequence ######################################################################### # set default position (DONE - 2014-12-09 - Hiram) # equivalent to felCat5 position obtained by liftOver test in # the browser from felCat5 default position (RHO gene) hgsql -e \ 'update dbDb set defaultPos="chrA2:54097485-54103554" where name="felCat8";' \ hgcentraltest ######################################################################### # all.joiner update, downloads and in pushQ - (DONE 2015-01-27 - Hiram) cd $HOME/kent/src/hg/makeDb/schema # fixup all.joiner until this is a clean output joinerCheck -database=felCat8 -keys all.joiner joinerCheck -database=felCat8 -tableCoverage all.joiner joinerCheck -database=felCat8 -times all.joiner cd /hive/data/genomes/felCat8 time makeDownloads.pl felCat8 > downloads.log 2>&1 # real 23m40.246s # now ready for pushQ entry mkdir /hive/data/genomes/felCat8/pushQ cd /hive/data/genomes/felCat8/pushQ # do not want transMap in the output: makePushQSql.pl felCat8 2> stderr.out | grep -v transMap > felCat8.pushQ.sql # check for errors in stderr.out, some are OK, e.g.: # WARNING: hgwdev does not have /gbdb/felCat8/wib/gc5Base.wib # WARNING: hgwdev does not have /gbdb/felCat8/wib/quality.wib # WARNING: hgwdev does not have /gbdb/felCat8/bbi/quality.bw # WARNING: felCat8 does not have seq # WARNING: felCat8 does not have extFile # copy it to hgwbeta scp -p felCat8.pushQ.sql qateam@hgwbeta:/tmp ssh qateam@hgwbeta './bin/x86_64/hgsql qapushq < /tmp/felCat8.pushQ.sql' # in that pushQ entry walk through each entry and see if the # sizes will set properly ######################################################################### # LIFTOVER TO felCat9 (DONE - 2018-02-28 - Hiram) ssh hgwdev mkdir /hive/data/genomes/felCat8/bed/blat.felCat9.2018-02-28 cd /hive/data/genomes/felCat8/bed/blat.felCat9.2018-02-28 time (doSameSpeciesLiftOver.pl -verbose=2 -buildDir=`pwd` \ -ooc=/hive/data/genomes/felCat8/jkStuff/felCat8.11.ooc \ -bigClusterHub=ku -dbHost=hgwdev -workhorse=hgwdev \ felCat8 felCat9) > do.log 2>&1 & # real 1047m54.841s # verify the convert link on the test browser is now active from felCat8 to # felCat9 #########################################################################