# for emacs: -*- mode: sh; -*- # This file describes browser build for the susScr11 # Pig -- Sus scrofa # chrMT listed in assembly == NC_000845.1 == AF034253.1 ############################################################################# # fetch sequence from new style download directory (DONE - 2017-07-25 - Hiram) mkdir -p /hive/data/genomes/susScr11/refseq cd /hive/data/genomes/susScr11/refseq time rsync -L -a -P \ rsync://ftp.ncbi.nlm.nih.gov/genomes/refseq/vertebrate_mammalian/Sus_scrofa/all_assembly_versions/GCF_000003025.6_Sscrofa11.1/ ./ # real 1m53.774s # sent 1483 bytes received 3015662916 bytes 26569730.39 bytes/sec # total size is 3015288899 speedup is 1.00 # measure what we have here: faSize GCF_000003025.6_Sscrofa11.1_genomic.fna.gz # 2501912388 bases (29864684 N's 2472047704 real 1576544146 upper # 895503558 lower) in 613 sequences in 1 files # Total size: mean 4081423.1 sd 23780904.1 min 15096 (NW_018085360.1) # max 274330532 (NC_010443.5) median 49329 # %35.79 masked total, %36.23 masked real faCount GCF_000003025.6_Sscrofa11.1_genomic.fna.gz | tail # #seq len A C G T N cpg # total 2501912388 717891230 517402066 517706165 719048243 29864684 30619972 ############################################################################# # fixup to UCSC naming scheme (DONE - 2017-07-25 - Hiram) mkdir /hive/data/genomes/susScr11/ucsc cd /hive/data/genomes/susScr11/ucsc # verify no duplicate sequences: time faToTwoBit ../refseq/*1_genomic.fna.gz refseq.2bit # real 1m13.138s twoBitDup refseq.2bit # should be silent output, otherwise the duplicates need to be removed time ~/kent/src/hg/utils/automation/ucscCompositeAgp.pl \ ../refseq/*1_genomic.fna.gz ../refseq/*_assembly_structure/Primary_Assembly NC_010443.5 chr1 NC_010444.4 chr2 NC_010445.4 chr3 NC_010446.5 chr4 NC_010447.5 chr5 NC_010448.4 chr6 NC_010449.5 chr7 NC_010450.4 chr8 NC_010451.4 chr9 NC_010452.4 chr10 NC_010453.5 chr11 NC_010454.4 chr12 NC_010455.5 chr13 NC_010456.5 chr14 NC_010457.5 chr15 NC_010458.4 chr16 NC_010459.5 chr17 NC_010460.4 chr18 NC_010461.5 chrX NC_010462.3 chrY real 14m57.924s time ~/kent/src/hg/utils/automation/unplacedWithChroms.pl \ ../refseq/*_assembly_structure/Primary_Assembly # processed 583 sequences into chrUn.fa.gz # real 0m21.149s time ~/kent/src/hg/utils/automation/unlocalizedWithChroms.pl \ ../refseq/*_assembly_structure/Primary_Assembly # Y # processed 9 sequences into chr*_random.gz 1 files # real 0m0.501s # bash syntax here mitoAcc=`grep MT ../refseq/GCF_000003025.6_Sscrofa11.1_assembly_report.txt | cut -f7` printf "# mitoAcc %s\n" "$mitoAcc" # mitoAcc NC_000845.1 zcat \ ../refseq/*_assembly_structure/non-nuclear/assem*/AGP/chrMT.comp.agp.gz \ | grep -v "^#" | sed -e "s/^$mitoAcc/chrM/;" > chrM.agp printf ">chrM\n" > chrM.fa twoBitToFa -noMask refseq.2bit:$mitoAcc stdout | grep -v "^>" >> chrM.fa gzip chrM.fa # verify fasta and AGP match: time faToTwoBit chr*.fa.gz test.2bit # real 1m7.749s cat *.agp | checkAgpAndFa stdin test.2bit 2>&1 | tail # All AGP and FASTA entries agree - both files are valid # verify nothing lost compared to genbank: time twoBitToFa test.2bit stdout | faSize stdin # 2501912388 bases (29864684 N's 2472047704 real 2472047704 upper 0 lower) # in 613 sequences in 1 files # Total size: mean 4081423.1 sd 23780904.1 min 15096 (chrUn_NW_018085360v1) # max 274330532 (chr1) median 49329 # same totals as above: # 2501912388 bases (29864684 N's 2472047704 real 1576544146 upper # 895503558 lower) in 613 sequences in 1 files # Total size: mean 4081423.1 sd 23780904.1 min 15096 (NW_018085360.1) # max 274330532 (NC_010443.5) median 49329 ############################################################################# # Initial database build (DONE - 2017-07-25 - Hiram) # same photoReference.txt as was used in susScr3: cd /hive/data/genomes/susScr11 cat ../susScr3/photoReference.txt photoCreditURL http://www.ars.usda.gov/is/graphics/photos/mar98/k7974-18.htm photoCreditName USDA Agricultural Research Service cp -p ../susScr3/photoReference.txt . # establish the config.ra file: ~/kent/src/hg/utils/automation/prepConfig.pl susScr11 mammal pig \ refseq/*_assembly_report.txt > susScr11.config.ra # verify this looks OK: cat susScr11.config.ra # config parameters for makeGenomeDb.pl: db susScr11 clade mammal scientificName Sus scrofa commonName Pig assemblyDate Feb. 2017 assemblyLabel The Swine Genome Sequencing Consortium (SGSC) assemblyShortLabel Sscrofa11.1 orderKey 16312 # mitochondrial sequence included in refseq release # mitoAcc NC_000845.1 mitoAcc none fastaFiles /hive/data/genomes/susScr11/ucsc/*.fa.gz agpFiles /hive/data/genomes/susScr11/ucsc/*.agp # qualFiles none dbDbSpeciesDir pig photoCreditURL http://www.ars.usda.gov/is/graphics/photos/mar98/k7974-18.htm photoCreditName USDA Agricultural Research Service ncbiGenomeId 84 ncbiAssemblyId 1004191 ncbiAssemblyName Sscrofa11.1 ncbiBioProject 13421 ncbiBioSample SAMN02953785 genBankAccessionID GCF_000003025.6 taxId 9823 # verify sequence and AGP are OK: time (makeGenomeDb.pl -workhorse=hgwdev -dbHost=hgwdev -fileServer=hgwdev \ -stop=agp susScr11.config.ra) > agp.log 2>&1 # real 2m14.138s # verify it ran OK: # *** All done! (through the 'agp' step) # then finish it off: time (~/kent/src/hg/utils/automation/makeGenomeDb.pl -workhorse=hgwdev \ -dbHost=hgwdev -fileServer=hgwdev -continue=db \ susScr11.config.ra ) > db.log 2>&1 # real 20m1.184s # XXX failed: # ssh -x -o 'StrictHostKeyChecking = no' -o 'BatchMode = yes' hgwdev hgsql -h localhost -A -N hgcentraltest < /cluster/data/susScr11/dbDbInsert.sql # HgStepManager: executing step 'trackDb' Tue Jul 25 10:43:10 2017. # makeLocalTrackDbRa: missing AGP gap type definition: repeat at /cluster/home/hiram/kent/src/hg/utils/automation/makeGenomeDb.pl line 1176, line 1. # new types of gap definitions: hgsql -e 'select type from gap;' susScr11 | sort | uniq -c 93 contig 2 repeat 233 scaffold hgsql -e 'select * from gap where type like "repeat";' susScr11 +-----+-------+------------+----------+-----+---+------+--------+--------+ | bin | chrom | chromStart | chromEnd | ix | n | size | type | bridge | +-----+-------+------------+----------+-----+---+------+--------+--------+ | 889 | chrY | 39921294 | 39926294 | 641 | N | 5000 | repeat | yes | | 890 | chrY | 40010306 | 40015306 | 647 | N | 5000 | repeat | yes | +-----+-------+------------+----------+-----+---+------+--------+--------+ # fixing the makeGenomeDb.pl script: time (~/kent/src/hg/utils/automation/makeGenomeDb.pl -workhorse=hgwdev \ -dbHost=hgwdev -fileServer=hgwdev -continue=trackDb \ susScr11.config.ra ) > trackDb.log 2>&1 # real 0m7.365s # check in the trackDb files created and add to trackDb/makefile # temporary symlink until after masking ln -s `pwd`/susScr11.unmasked.2bit /gbdb/susScr11/susScr11.2bit ############################################################################# # cytoBandIdeo - (DONE - 2017-07-25 - Hiram) mkdir /hive/data/genomes/susScr11/bed/cytoBand cd /hive/data/genomes/susScr11/bed/cytoBand makeCytoBandIdeo.csh susScr11 ############################################################################## # cpgIslands on UNMASKED sequence (DONE - 2017-07-25 - Hiram) mkdir /hive/data/genomes/susScr11/bed/cpgIslandsUnmasked cd /hive/data/genomes/susScr11/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/susScr11/susScr11.unmasked.2bit \ -workhorse=hgwdev -smallClusterHub=ku susScr11) > do.log 2>&1 # real 5m34.816s cat fb.susScr11.cpgIslandExtUnmasked.txt # 44748680 bases of 2472073034 (1.810%) in intersection ############################################################################# # running repeat masker (DONE - 2017-07-25 - Hiram) mkdir /hive/data/genomes/susScr11/bed/repeatMasker cd /hive/data/genomes/susScr11/bed/repeatMasker time (doRepeatMasker.pl -buildDir=`pwd` \ -bigClusterHub=ku -dbHost=hgwdev -workhorse=hgwdev \ -smallClusterHub=ku susScr11) > do.log 2>&1 & # real 781m8.842s cat faSize.rmsk.txt # 2501912388 bases (29864684 N's 2472047704 real 1352527731 upper # 1119519973 lower) in 613 sequences in 1 files # Total size: mean 4081423.1 sd 23780904.1 min 15096 (chrUn_NW_018085360v1) # max 274330532 (chr1) median 49329 # %44.75 masked total, %45.29 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 susScr11 rmsk # 1119521852 bases of 2501912388 (44.747%) in intersection # real 0m42.868s # 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 # faster way to get the same result: time hgsql -N -e 'select genoName,genoStart,genoEnd from rmsk;' susScr11 \ | bedSingleCover.pl stdin | ave -col=4 stdin | grep "^total" # total 1119521852.000000 # real 0m35.755s ########################################################################## # running simple repeat (DONE - 2017-07-25 - Hiram) mkdir /hive/data/genomes/susScr11/bed/simpleRepeat cd /hive/data/genomes/susScr11/bed/simpleRepeat time (doSimpleRepeat.pl -buildDir=`pwd` -bigClusterHub=ku \ -dbHost=hgwdev -workhorse=hgwdev -smallClusterHub=ku \ -trf409 5 susScr11) > do.log 2>&1 & # real 9m56.089s cat fb.simpleRepeat # 33056801 bases of 2472073034 (1.337%) in intersection # add to this simple repeat to rmsk: cd /hive/data/genomes/susScr11 twoBitMask susScr11.rmsk.2bit \ -add bed/simpleRepeat/trfMask.bed susScr11.2bit # you can safely ignore the warning about fields >= 13 twoBitToFa susScr11.2bit stdout | faSize stdin > faSize.susScr11.2bit.txt cat faSize.susScr11.2bit.txt # 2501912388 bases (29864684 N's 2472047704 real 1351491909 upper # 1120555795 lower) in 613 sequences in 1 files # Total size: mean 4081423.1 sd 23780904.1 # min 15096 (chrUn_NW_018085360v1) max 274330532 (chr1) median 49329 # %44.79 masked total, %45.33 masked real rm /gbdb/susScr11/susScr11.2bit ln -s `pwd`/susScr11.2bit /gbdb/susScr11/susScr11.2bit ############################################################################# # CREATE MICROSAT TRACK (DONE - 2017-07-27 - Hiram) ssh hgwdev mkdir /cluster/data/susScr11/bed/microsat cd /cluster/data/susScr11/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 susScr11 microsat microsat.bed ############################################################################# # ucscToINSDC table/track (DONE - 2017-07-29 - Hiram) # the sequence here is working for a 'refseq' assembly with a chrM # situation may be specific depending upon what is available in the assembly mkdir /hive/data/genomes/susScr11/bed/ucscToINSDC cd /hive/data/genomes/susScr11/bed/ucscToINSDC # find accession for chrM grep chrM ../../susScr11.agp # chrM 1 16613 1 O NC_000845.1 1 16613 + # use that accession here: ~/kent/src/hg/utils/automation/ucscToINSDC.sh \ ../../refseq/GCF_*structure/Primary_Assembly NC_000845.1 # this is actually ucscToRefSeq sort -k2 ucscToINSDC.txt > ucscToRefSeq.txt rm -f ucscToINSDC.txt awk '{printf "%s\t%s\n", $2, $1}' ucscToRefSeq.txt | sort > refseqToUcsc.txt # there is no INSDC name in the assembly_report for chrM/NC_000845.1 # use the INSDC name from before: AF034253.1 grep -v "^#" ../../refseq/GCF*_assembly_report.txt | cut -f5,7 \ | sed -e 's/na\b/AF034253.1/;' | awk '{printf "%s\t%s\n", $2, $1}' \ | sort > refseq.insdc.txt # the sed \b means to match word awk '{printf "%s\t0\t%d\n", $1,$2}' ../../chrom.sizes \ | sort > name.coordinate.tab # the tr commands avoid the problem of trying to use the -t argument # to the join command which doesn't accept -t'\t' but instead has # to use the unseen/can not copy command ctrl-v i join -2 2 refseq.insdc.txt ucscToRefSeq.txt | tr '[ ]' '[\t]' | sort -k3 \ | join -2 3 name.coordinate.tab - | tr '[ ]' '[\t]' | cut -f1-3,5 \ > ucscToINSDC.bed join -2 2 refseq.insdc.txt ucscToRefSeq.txt | tr '[ ]' '[\t]' | sort -k3 \ | join -2 3 name.coordinate.tab - | tr '[ ]' '[\t]' | cut -f1-4 \ > ucscToRefSeq.bed # verify chrM is correct: grep chrM *.bed # ucscToINSDC.bed:chrM 0 16613 AF034253.1 # ucscToRefSeq.bed:chrM 0 16613 NC_000845.1 # should be same line counts throughout: wc -l * # 613 name.coordinate.tab # 613 refseq.insdc.txt # 613 ucscToINSDC.bed # 613 ucscToRefSeq.bed # 613 ucscToRefSeq.txt cut -f1 ucscToINSDC.bed | awk '{print length($0)}' | sort -n | tail -1 # 26 # use the 26 in this sed sed -e "s/21/26/" $HOME/kent/src/hg/lib/ucscToINSDC.sql \ | hgLoadSqlTab susScr11 ucscToINSDC stdin ucscToINSDC.bed cut -f1 ucscToRefSeq.bed | awk '{print length($0)}' | sort -n | tail -1 sed -e "s/21/26/" $HOME/kent/src/hg/lib/ucscToINSDC.sql \ | hgLoadSqlTab susScr11 ucscToRefSeq stdin ucscToRefSeq.bed checkTableCoords susScr11 # should cover %100 entirely: featureBits -countGaps susScr11 ucscToINSDC # 2501912388 bases of 2501912388 (100.000%) in intersection featureBits -countGaps susScr11 ucscToRefSeq # 2501912388 bases of 2501912388 (100.000%) in intersection ######################################################################### # add chromAlias table (DONE - 2017-07-29 - Hiram) mkdir /hive/data/genomes/susScr11/bed/chromAlias cd /hive/data/genomes/susScr11/bed/chromAlias hgsql -N -e 'select chrom,name,"refseq" from ucscToRefSeq;' susScr11 \ > ucsc.refseq.tab hgsql -N -e 'select chrom,name,"genbank" from ucscToINSDC;' susScr11 \ > ucsc.genbank.tab # verify chrM is correct: grep chrM * # ucsc.genbank.tab:chrM AF034253.1 genbank # ucsc.refseq.tab:chrM NC_000845.1 refseq awk '{printf "%s\t%s\t%s\n", $2,$1,$3}' ucsc.genbank.tab ucsc.refseq.tab \ | sort > susScr11.chromAlias.tab hgLoadSqlTab susScr11 chromAlias ~/kent/src/hg/lib/chromAlias.sql \ susScr11.chromAlias.tab ######################################################################### # fixup search rule for assembly track/gold table (DONE - 2017-07-29 - Hiram) cd ~/kent/src/hg/makeDb/trackDb/pig/susScr11 # preview prefixes and suffixes: hgsql -N -e "select frag from gold;" susScr11 \ | sed -e 's/[0-9][0-9]*//;' | sort | uniq -c 705 AEMK.1 2 AJKK.1 2 CU.2 18 FO.1 234 FO.2 105 FO.3 52 FO.4 12 FO.5 3 FO.6 1 FO.7 1 FO.9 1 FP.2 1 FP.3 7 FQ.1 91 FQ.2 55 FQ.3 9 FQ.4 10 FQ.5 2 FQ.6 1 FQ.9 1 NC_.1 # implies a search rule of: '[ACFN][CEJOPQU][MK0-9_]+(\.[0-9]+)?' # verify this rule will find them all or eliminate them all: hgsql -N -e "select frag from gold;" susScr11 | wc -l # 1313 hgsql -N -e "select frag from gold;" susScr11 \ | egrep -e '[ACFN][CEJOPQU][MK0-9_]+(\.[0-9]+)?' | wc -l # 1313 hgsql -N -e "select frag from gold;" susScr11 \ | egrep -v -e '[ACFN][CEJOPQU][MK0-9_]+(\.[0-9]+)?' | wc -l # 0 # hence, add to trackDb/rhesus/susScr11/trackDb.ra searchTable gold shortCircuit 1 termRegex [ACFN][CEJOPQU][MK0-9_]+(\.[0-9]+)? query select chrom,chromStart,chromEnd,frag from %s where frag like '%s%%' searchPriority 8 git commit -m 'add gold table search rule refs #19859' trackDb.ra # verify searches work in the position box ########################################################################## ## WINDOWMASKER (DONE - 2017-07-27 - Hiram) mkdir /hive/data/genomes/susScr11/bed/windowMasker cd /hive/data/genomes/susScr11/bed/windowMasker time (doWindowMasker.pl -buildDir=`pwd` -workhorse=hgwdev \ -dbHost=hgwdev susScr11) > do.log 2>&1 # real 158m14.091s # Masking statistics cat faSize.susScr11.cleanWMSdust.txt # 2501912388 bases (29864684 N's 2472047704 real 1563211996 upper # 908835708 lower) in 613 sequences in 1 files # Total size: mean 4081423.1 sd 23780904.1 min 15096 (chrUn_NW_018085360v1) # max 274330532 (chr1) median 49329 # %36.33 masked total, %36.76 masked real cat fb.susScr11.rmsk.windowmaskerSdust.txt # 677163594 bases of 2501912388 (27.066%) in intersection ########################################################################## # cpgIslands - (DONE - 2017-07-27 - Hiram) mkdir /hive/data/genomes/susScr11/bed/cpgIslands cd /hive/data/genomes/susScr11/bed/cpgIslands time (doCpgIslands.pl -dbHost=hgwdev -bigClusterHub=ku \ -workhorse=hgwdev -smallClusterHub=ku susScr11) > do.log 2>&1 # real 4m52.080s cat fb.susScr11.cpgIslandExt.txt # 32550865 bases of 2472073034 (1.317%) in intersection ############################################################################## # ncbiRefSeq gene track (TBD - 2016-05-05 - Hiram) mkdir /hive/data/genomes/susScr11/bed/ncbiRefSeq cd /hive/data/genomes/susScr11/bed/ncbiRefSeq # working on this script, running step by step: time (/cluster/home/hiram/kent/src/hg/utils/automation/doNcbiRefSeq.pl \ -stop=download -buildDir=`pwd` -bigClusterHub=ku \ -fileServer=hgwdev -workhorse=hgwdev -smallClusterHub=ku -dbHost=hgwdev \ refseq vertebrate_mammalian Pan_paniscus \ GCF_000258655.2_panpan1.1 susScr11) > download.log 2>&1 # real 12m36.320s time (/cluster/home/hiram/kent/src/hg/utils/automation/doNcbiRefSeq.pl \ -continue=process -stop=process -buildDir=`pwd` -bigClusterHub=ku \ -fileServer=hgwdev -workhorse=hgwdev -smallClusterHub=ku -dbHost=hgwdev \ refseq vertebrate_mammalian Pan_paniscus \ GCF_000258655.2_panpan1.1 susScr11) > process.log 2>&1 # real 4m22.621s time (/cluster/home/hiram/kent/src/hg/utils/automation/doNcbiRefSeq.pl \ -continue=load -stop=load -buildDir=`pwd` -bigClusterHub=ku \ -fileServer=hgwdev -workhorse=hgwdev -smallClusterHub=ku -dbHost=hgwdev \ refseq vertebrate_mammalian Pan_paniscus \ GCF_000258655.2_panpan1.1 susScr11) > load.log 2>&1 # real 0m21.690s cat fb.ncbiRefSeq.susScr11.txt # 74646536 bases of 2725937399 (2.738%) in intersection ############################################################################## # genscan - (DONE - 2017-07-27 - Hiram) mkdir /hive/data/genomes/susScr11/bed/genscan cd /hive/data/genomes/susScr11/bed/genscan time (doGenscan.pl -buildDir=`pwd` -workhorse=hgwdev -dbHost=hgwdev \ -bigClusterHub=ku susScr11) > do.log 2>&1 # real 737m1.735s cat fb.susScr11.genscan.txt # 55049663 bases of 2472073034 (2.227%) in intersection cat fb.susScr11.genscanSubopt.txt # 48834412 bases of 2472073034 (1.975%) in intersection ############################################################################# # augustus gene track (DONE - 2017-07-27 - Hiram) mkdir /hive/data/genomes/susScr11/bed/augustus cd /hive/data/genomes/susScr11/bed/augustus time (doAugustus.pl -buildDir=`pwd` -bigClusterHub=ku \ -species=human -dbHost=hgwdev \ -workhorse=hgwdev susScr11) > do.log 2>&1 # real 207m36.088s cat fb.susScr11.augustusGene.txt # 47127389 bases of 2472073034 (1.906%) in intersection ############################################################################# # Create kluster run files (DONE - 2017-07-27 - Hiram) # numerator is susScr11 gapless bases "real" as reported by: featureBits -noRandom -noHap susScr11 gap # 29824354 bases of 2405454322 (1.240%) 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 \( 2405454322 / 2861349177 \) \* 1024 # ( 2405454322 / 2861349177 ) * 1024 = 860.847479 # ==> use -repMatch=800 according to size scaled down from 1024 for human. # and rounded down to nearest 100 cd /hive/data/genomes/susScr11 time blat susScr11.2bit \ /dev/null /dev/null -tileSize=11 -makeOoc=jkStuff/susScr11.11.ooc \ -repMatch=800 # Wrote 34181 overused 11-mers to jkStuff/susScr11.11.ooc # real 0m44.366s # check non-bridged gaps to see what the typical size is: hgsql -N \ -e 'select * from gap where bridge="no" order by size;' susScr11 \ | sort -k7,7nr # minimum size is 50000 gapToLift -verbose=2 -minGap=50000 susScr11 \ jkStuff/susScr11.nonBridged.lft -bedFile=jkStuff/susScr11.nonBridged.bed ######################################################################### # LIFTOVER TO susScr3 (DONE - 2017-07-27 - Hiram ) mkdir /hive/data/genomes/susScr11/bed/blat.susScr3.2017-07-27 cd /hive/data/genomes/susScr11/bed/blat.susScr3.2017-07-27 # -debug run to create run dir, preview scripts... doSameSpeciesLiftOver.pl -debug \ -ooc /hive/data/genomes/susScr11/jkStuff/susScr11.11.ooc \ susScr11 susScr3 # Real run: time (doSameSpeciesLiftOver.pl -verbose=2 \ -ooc /hive/data/genomes/susScr11/jkStuff/susScr11.11.ooc \ -bigClusterHub=ku -dbHost=hgwdev -workhorse=hgwdev \ susScr11 susScr3) > do.log 2>&1 & # real 252m20.235s # verify browser can run a view in other genomes to susScr3 from susScr11 ######################################################################### # lastz/chain/net swap from hg38 (DONE - 2017-08-02 - Hiram) # alignment to hg38 cd /hive/data/genomes/hg38/bed/lastzSusScr11.2017-07-31 cat fb.hg38.chainSusScr11Link.txt # 1463754915 bases of 3049335806 (48.002%) in intersection # and for the swap: mkdir /hive/data/genomes/susScr11/bed/blastz.hg38.swap cd /hive/data/genomes/susScr11/bed/blastz.hg38.swap time (doBlastzChainNet.pl -verbose=2 \ /hive/data/genomes/hg38/bed/lastzSusScr11.2017-07-31/DEF \ -swap -chainMinScore=3000 -chainLinearGap=medium \ -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \ -syntenicNet) > swap.log 2>&1 # real 107m7.364s cat fb.susScr11.chainHg38Link.txt # 1387973267 bases of 2472073034 (56.146%) in intersection time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` susScr11 hg38) \ > rbest.log 2>&1 # real 598m8.675s ######################################################################### # lastz/chain/net swap from mm10 (DONE - 2017-08-02 - Hiram) # alignment on mm10 cd /hive/data/genomes/mm10/bed/lastzSusScr11.2017-07-31 cat fb.mm10.chainSusScr11Link.txt # 731012356 bases of 2652783500 (27.556%) in intersection mkdir /hive/data/genomes/susScr11/bed/blastz.mm10.swap cd /hive/data/genomes/susScr11/bed/blastz.mm10.swap time (doBlastzChainNet.pl -verbose=2 \ /hive/data/genomes/mm10/bed/lastzSusScr11.2017-07-31/DEF \ -swap -syntenicNet \ -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \ -chainMinScore=3000 -chainLinearGap=medium) > swap.log 2>&1 # real 61m6.153s cat fb.susScr11.chainMm10Link.txt # 715277290 bases of 2472073034 (28.934%) in intersection time (doRecipBest.pl -workhorse=hgwdev susScr11 mm10 \ -buildDir=`pwd` -workhorse=hgwdev) > rbest.log 2>&1 & # real 358m15.340s ############################################################################## # GENBANK AUTO UPDATE (DONE - 2017-07-29 - Hiram) ssh hgwdev cd $HOME/kent/src/hg/makeDb/genbank git pull # /cluster/data/genbank/data/organism.lst shows: # organism mrnaCnt estCnt refSeqCnt # Sus scrofa 41240 1676416 4173 # edit etc/genbank.conf to add susScr11 just before susScr3 # susScr11 (pig) susScr11.serverGenome = /hive/data/genomes/susScr11/susScr11.2bit susScr11.clusterGenome = /hive/data/genomes/susScr11/susScr11.2bit susScr11.ooc = /hive/data/genomes/susScr11/jkStuff/susScr11.11.ooc susScr11.lift = /hive/data/genomes/susScr11/jkStuff/susScr11.nonBridged.lft susScr11.perChromTables = no susScr11.refseq.mrna.native.pslCDnaFilter = ${finished.refseq.mrna.native.pslCDnaFilter} susScr11.refseq.mrna.xeno.pslCDnaFilter = ${finished.refseq.mrna.xeno.pslCDnaFilter} susScr11.genbank.mrna.native.pslCDnaFilter = ${finished.genbank.mrna.native.pslCDnaFilter} susScr11.genbank.mrna.xeno.pslCDnaFilter = ${finished.genbank.mrna.xeno.pslCDnaFilter} susScr11.genbank.est.native.pslCDnaFilter = ${finished.genbank.est.native.pslCDnaFilter} susScr11.genbank.est.xeno.pslCDnaFilter = ${finished.genbank.est.xeno.pslCDnaFilter} susScr11.downloadDir = susScr11 susScr11.refseq.mrna.native.load = yes susScr11.refseq.mrna.xeno.load = yes # DO NOT NEED genbank.mrna.xeno except for human, mouse susScr11.genbank.mrna.xeno.load = yes susScr11.genbank.mrna.xeno.loadDesc = no susScr11.genbank.est.native.load = yes # susScr11.upstreamGeneTbl = ensGene # susScr11.upstreamMaf = multiz12way # /hive/data/genomes/susScr11/bed/multiz12way/species.list git commit -m "Added susScr11; refs #19879" 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 susScr11 # logFile: var/build/logs/2017.07.27-20:49:34.susScr11.initalign.log # real 1486m19.233s tail -2 var/build/logs/2017.07.27-20:49:34.susScr11.initalign.log # hgwdev 2017.07.28-21:20:42 susScr11.initalign: Succeeded: susScr11 # hgwdev 2017.07.28-21:35:53 susScr11.initalign: finish # To re-do, rm the dir first: # /cluster/data/genbank/work/initial.susScr11 # load database when finished ssh hgwdev cd /cluster/data/genbank time ./bin/gbDbLoadStep -drop -initialLoad susScr11 # logFile: var/dbload/hgwdev/logs/2017.07.29-07:05:26.susScr11.dbload.log # real 81m41.107s tail -1 var/dbload/hgwdev/logs/2017.07.29-07:05:26.susScr11.dbload.log # hgwdev 2017.07.29-08:27:07 susScr11.dbload: finish # enable daily alignment and update of hgwdev cd ~/kent/src/hg/makeDb/genbank git pull # add susScr11 to: # etc/align.dbs etc/hgwdev.dbs git add etc/align.dbs etc/hgwdev.dbs git commit -m "Added susScr11 - pig refs #19859" etc/align.dbs etc/hgwdev.dbs git push make etc-update ############################################################################## # BLATSERVERS ENTRY (DONE - 2017-08-03 - 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 ("susScr11", "blat1b", "17880", "1", "0"); \ INSERT INTO blatServers (db, host, port, isTrans, canPcr) \ VALUES ("susScr11", "blat1b", "17881", "0", "1");' \ hgcentraltest # test it with some sequence ############################################################################## # set default position to OPN1SW gene displays (DONE - 2017-08-03 - Hiram) # same as susScr3: hgsql -e \ 'update dbDb set defaultPos="chr18:19836295-19840119" where name="susScr11";' \ hgcentraltest ############################################################################## # all.joiner update, downloads and in pushQ - (DONE - 2017-08-03 - Hiram) cd $HOME/kent/src/hg/makeDb/schema # fixup all.joiner until this is a clean output joinerCheck -database=susScr11 -tableCoverage all.joiner joinerCheck -database=susScr11 -times all.joiner joinerCheck -database=susScr11 -keys all.joiner cd /hive/data/genomes/susScr11 time (makeDownloads.pl susScr11) > downloads.log 2>&1 # real 17m8.716s # now ready for pushQ entry mkdir /hive/data/genomes/susScr11/pushQ cd /hive/data/genomes/susScr11/pushQ time (makePushQSql.pl -redmineList susScr11) \ > susScr11.pushQ.sql 2> stderr.out # real 3m46.855s # check for errors in stderr.out, some are OK, e.g.: # writing redmine listings to # redmine.susScr11.file.list # redmine.susScr11.table.list # redmine.susScr11.releaseLog.txt # WARNING: susScr11 does not have seq # WARNING: susScr11 does not have extFile #########################################################################