# for emacs: -*- mode: sh; -*- # This file describes browser build for the panTro6 ######################################################################### # reuse photograph from panTro5 previous versions # (DONE - 2018-03-23 - Hiram) mkdir /hive/data/genomes/panTro6 cd /hive/data/genomes/panTro6 cp -p ../panTro5/photoReference.txt . cat photoReference.txt photoCreditURL http://www.smm.org/ photoCreditName Science Museum of Minnesota ######################################################################### # Initial steps (DONE - 2018-03-23 - Hiram) # To start this initialBuild.txt document, from a previous assembly document: mkdir ~/kent/src/hg/makeDb/doc/panTro6 cd ~/kent/src/hg/makeDb/doc/panTro6 # best to use a most recent document since it has the latest features and # procedures: sed -e 's/felCat9/panTro6/g; s/FelCat9/PanTro6/g; s/DONE/TBD/g;' ../felCat9/initialBuild.txt > initialBuild.txt mkdir /hive/data/genomes/panTro6/refseq cd /hive/data/genomes/panTro6/refseq time rsync -L -a -P \ rsync://ftp.ncbi.nlm.nih.gov/genomes/refseq/vertebrate_mammalian/Pan_troglodytes/all_assembly_versions/GCF_002880755.1_Clint_PTRv2/ ./ # sent 3106 bytes received 4399985960 bytes 18219416.42 bytes/sec # total size is 4399437472 speedup is 1.00 # real 4m0.842s # check assembly size for later reference: faSize G*_PTRv2_genomic.fna.gz # 3050398082 bases (31805092 N's 3018592990 real 1820051887 upper # 1198541103 lower) in 4346 sequences in 1 files # Total size: mean 701886.4 sd 9434013.2 min 223 (NW_019937062.1) # max 224244399 (NC_036879.1) median 29187 # %39.29 masked total, %39.71 masked real # this information is from the top of # panTro6/refseq/GCF_002880755.1_Clint_PTRv2_assembly_report.txt # Assembly name: Clint_PTRv2 # Organism name: Pan troglodytes (chimpanzee) # Isolate: Yerkes chimp pedigree #C0471 (Clint) # Sex: male # Taxid: 9598 # BioSample: SAMN06272697 # BioProject: PRJNA369439 # Submitter: University of Washington # Date: 2018-1-19 # Assembly type: haploid # Release type: major # Assembly level: Chromosome # Genome representation: full # WGS project: NBAG03 # Expected final version: yes # Genome coverage: 124x # RefSeq assembly accession: GCF_002880755.1 # ## Assembly-Units: ## GenBank Unit Accession RefSeq Unit Accession Assembly-Unit name ## GCF_002880765.1 Primary Assembly ## GCF_000001485.1 non-nuclear ############################################################################# # establish config.ra file (DONE - Hiram - 2018-03-23) # arguments here are: cd /hive/data/genomes/panTro6 $HOME/kent/src/hg/utils/automation/prepConfig.pl panTro6 mammal \ chimp ./refseq/*_assembly_report.txt > panTro6.config.ra # compare to ../panTro5 to see what might need to be fixed up: diff panTro6.config.ra ../panTro5/panTro5.config.ra | less # reset commonName Chimpanzee to: commonName Chimp # reset orderKey 3337 to: orderKey 3325 # reset ncbiGenomeId 325 to: ncbiGenomeId 202 # verify it looks sane cat panTro6.config.ra # config parameters for makeGenomeDb.pl: db panTro6 clade mammal genomeCladePriority 35 scientificName Pan troglodytes commonName Chimp assemblyDate Jan. 2018 assemblyLabel University of Washington assemblyShortLabel Clint_PTRv2 orderKey 3325 # mitochondrial sequence included in refseq release # mitoAcc NC_001643.1 mitoAcc none fastaFiles /hive/data/genomes/panTro6/ucsc/*.fa.gz agpFiles /hive/data/genomes/panTro6/ucsc/*.agp # qualFiles none dbDbSpeciesDir chimp photoCreditURL http://www.smm.org/ photoCreditName Science Museum of Minnesota ncbiGenomeId 202 ncbiAssemblyId 1642151 ncbiAssemblyName Clint_PTRv2 ncbiBioProject 369439 ncbiBioSample SAMN06272697 genBankAccessionID GCF_002880755.1 taxId 9598 ############################################################################# # setup UCSC named files (DONE - 2018-03-23 - Hiram) mkdir /hive/data/genomes/panTro6/ucsc cd /hive/data/genomes/panTro6/ucsc # check for duplicate sequences: time faToTwoBit -noMask ../refseq/G*_PTRv2_genomic.fna.gz refseq.2bit # real 1m17.463s twoBitDup refseq.2bit # no output is a good result, otherwise, would have to eliminate duplicates # the scripts creating the fasta here will be using this refseq.2bit file time ~/kent/src/hg/utils/automation/ucscCompositeAgp.pl \ ../refseq/G*_PTRv2_genomic.fna.gz \ ../refseq/G*_PTRv2_assembly_structure/Primary_Assembly # NC_006492.4 chrY # NC_036879.1 chr1 # NC_036880.1 chr2A # NC_036881.1 chr2B # NC_036882.1 chr3 # NC_036883.1 chr4 # NC_036884.1 chr5 # NC_036885.1 chr6 # NC_036886.1 chr7 # NC_036887.1 chr8 # NC_036888.1 chr9 # NC_036889.1 chr10 # NC_036890.1 chr11 # NC_036891.1 chr12 # NC_036892.1 chr13 # NC_036893.1 chr14 # NC_036894.1 chr15 # NC_036895.1 chr16 # NC_036896.1 chr17 # NC_036897.1 chr18 # NC_036898.1 chr19 # NC_036899.1 chr20 # NC_036900.1 chr21 # NC_036901.1 chr22 # NC_036902.1 chrX # real 16m9.446s # unplaced sequences time ~/kent/src/hg/utils/automation/unplacedWithChroms.pl \ ../refseq/*_assembly_structure/Primary_Assembly # processed 4316 sequences into chrUn.fa.gz # real 0m44.310s # unlocalized sequences time ~/kent/src/hg/utils/automation/unlocalizedWithChroms.pl \ ../refseq/*_assembly_structure/Primary_Assembly # 16 # 5 # processed 4 sequences into chr*_random.gz 2 files # real 0m6.591s # bash syntax here mitoAcc=`grep "^# mitoAcc" ../panTro6.config.ra | awk '{print $NF}'` printf "# mitoAcc %s\n" "$mitoAcc" # mitoAcc NC_001643.1 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 AGPs agree time faToTwoBit *.fa.gz test.2bit # real 1m22.353s time cat *.agp | checkAgpAndFa stdin test.2bit 2>&1 | tail -4 # All AGP and FASTA entries agree - both files are valid # real 0m10.242s # and no sequence lost from orginal: twoBitToFa test.2bit stdout | faSize stdin # 3050398082 bases (31805092 N's 3018592990 real 3018592990 upper 0 lower) # in 4346 sequences in 1 files # Total size: mean 701886.4 sd 9434013.2 min 223 (chrUn_NW_019937062v1) # max 224244399 (chr1) median 29187 # same numbers as above # 3050398082 bases (31805092 N's 3018592990 real 1820051887 upper # 1198541103 lower) in 4346 sequences in 1 files # Total size: mean 701886.4 sd 9434013.2 min 223 (NW_019937062.1) # max 224244399 (NC_036879.1) median 29187 # no longer need these temporary 2bit files rm refseq.2bit test.2bit ############################################################################# # Initial database build (DONE - 2018-03-23 - Hiram) cd /hive/data/genomes/panTro6 # verify sequence and AGP are OK: time (makeGenomeDb.pl -workhorse=hgwdev -dbHost=hgwdev -fileServer=hgwdev \ -stop=agp panTro6.config.ra) > agp.log 2>&1 # real 2m43.743s # verify there was no error in that step: tail agp.log # *** All done! (through the 'agp' step) # then finish it off: time (makeGenomeDb.pl -workhorse=hgwdev -dbHost=hgwdev \ -fileServer=hgwdev -continue=db panTro6.config.ra) > db.log 2>&1 # real 24m48.575s # verify gaps are all there: twoBitInfo -nBed panTro6.unmasked.2bit stdout | awk '{print $3-$2}' \ | ave stdin | sed -e 's/^/# /;' # Q1 100.000000 # median 499.000000 # Q3 50212.500000 # average 44482.646154 # min 10.000000 # max 621330.000000 # count 715 # total 31805092.000000 hgsql -e 'select chromEnd-chromStart from gap;' panTro6 | ave stdin | sed -e 's/^/# /;' # Q1 100.000000 # median 499.000000 # Q3 50212.500000 # average 44482.646154 # min 10.000000 # max 621330.000000 # count 715 # total 31805092.000000 # check in the trackDb files created in TemporaryTrackDbCheckout/ # and add panTro6 to trackDb/makefile # temporary symlink until masked sequence is available cd /hive/data/genomes/panTro6 ln -s `pwd`/panTro6.unmasked.2bit /gbdb/panTro6/panTro6.2bit ############################################################################## # cpgIslands on UNMASKED sequence (DONE - 2018-03-24 - Hiram) mkdir /hive/data/genomes/panTro6/bed/cpgIslandsUnmasked cd /hive/data/genomes/panTro6/bed/cpgIslandsUnmasked time (doCpgIslands.pl -dbHost=hgwdev -bigClusterHub=ku -buildDir=`pwd` \ -tableName=cpgIslandExtUnmasked \ -maskedSeq=/hive/data/genomes/panTro6/panTro6.unmasked.2bit \ -workhorse=hgwdev -smallClusterHub=ku panTro6) > do.log 2>&1 # real 6m17.200s cat fb.panTro6.cpgIslandExtUnmasked.txt # 29545528 bases of 3018592990 (0.979%) in intersection ############################################################################# # cytoBandIdeo - (DONE - 2018-03-24 - Hiram) mkdir /hive/data/genomes/panTro6/bed/cytoBand cd /hive/data/genomes/panTro6/bed/cytoBand makeCytoBandIdeo.csh panTro6 ############################################################################# # gapOverlap (DONE - 2018-03-24 - Hiram) mkdir /hive/data/genomes/panTro6/bed/gapOverlap cd /hive/data/genomes/panTro6/bed/gapOverlap time (doGapOverlap.pl \ -twoBit=/hive/data/genomes/panTro6/panTro6.unmasked.2bit panTro6 ) \ > do.log 2>&1 # real 14m5.164s cat fb.panTro6.gapOverlap.txt # 6998 bases of 3050398082 (0.000%) in intersection # only six items: zcat *.bed.gz | cut -f1-5 # chr12 113245358 113246724 chr12:113245359-113246724 633 # chr21 18867677 18869111 chr21:18867678-18869111 667 # chr8 127452459 127454559 chr8:127452460-127454559 1000 # chrX 52589209 52609380 chrX:52589210-52609380 1000 # chrY 7097196 7097619 chrY:7097197-7097619 199 ############################################################################# # tandemDups (DONE - 2018-03-24 - Hiram) mkdir /hive/data/genomes/panTro6/bed/tandemDups cd /hive/data/genomes/panTro6/bed/tandemDups time (~/kent/src/hg/utils/automation/doTandemDup.pl \ -twoBit=/hive/data/genomes/panTro6/panTro6.unmasked.2bit panTro6) \ > do.log 2>&1 & # real 96m33.185s cat fb.panTro6.tandemDups.txt # 133769723 bases of 3050398082 (4.385%) in intersection bigBedInfo panTro6.tandemDups.bb | sed -e 's/^/# /;' # version: 4 # fieldCount: 13 # hasHeaderExtension: yes # isCompressed: yes # isSwapped: 0 # extraIndexCount: 0 # itemCount: 2,570,600 # primaryDataSize: 65,661,880 # primaryIndexSize: 259,136 # zoomLevels: 9 # chromCount: 4134 # basesCovered: 1,636,830,812 # meanDepth (of bases covered): 12.911632 # minDepth: 1.000000 # maxDepth: 474.000000 # std of depth: 28.418142 ############################################################################# # run up idKeys files for chromAlias/ncbiRefSeq (DONE - 2018-03-24 - Hiram) mkdir /hive/data/genomes/panTro6/bed/idKeys cd /hive/data/genomes/panTro6/bed/idKeys time (doIdKeys.pl \ -twoBit=/hive/data/genomes/panTro6/panTro6.unmasked.2bit \ -buildDir=`pwd` panTro6) > do.log 2>&1 & # real 3m56.622s cat panTro6.keySignature.txt # d56a60e851e19f2c5b842c27bb43b990 ############################################################################# # ucscToINSDC and ucscToRefSeq table/track (DONE - 2018-03-24 - Hiram) # the sequence here is working for a 'refseq' assembly # beware of a chrM situation may be specific depending upon what is # available in the assembly mkdir /hive/data/genomes/panTro6/bed/ucscToINSDC cd /hive/data/genomes/panTro6/bed/ucscToINSDC join -t$'\t' ../idKeys/panTro6.idKeys.txt \ ../../refseq/idKeysGenbank/genbankPanTro6.idKeys.txt | cut -f2- \ | sort -k1,1 | join -t$'\t' <(sort -k1,1 ../../chrom.sizes) - \ | awk '{printf "%s\t0\t%d\t%s\n", $1, $2, $3}' \ | sort -k1,1 -k2,2n > ucscToINSDC.bed join -t$'\t' ../idKeys/panTro6.idKeys.txt \ ../../refseq/idKeys/refseqPanTro6.idKeys.txt | cut -f2- \ | sort -k1,1 | join -t$'\t' <(sort -k1,1 ../../chrom.sizes) - \ | awk '{printf "%s\t0\t%d\t%s\n", $1, $2, $3}' \ | sort -k1,1 -k2,2n > ucscToRefSeq.bed # verify line counts are the same wc -l *.bed ../../chrom.sizes # 4344 ucscToINSDC.bed # 4346 ucscToRefSeq.bed # 4346 ../../chrom.sizes # need to find INSDC equivalents for chrY and chrM: egrep "chrY|chrM" * ucscToRefSeq.bed:chrM 0 16554 NC_001643.1 ucscToRefSeq.bed:chrY 0 26350515 NC_006492.4 # lookup those accessions at NCBI Entrez # NC_001643.1 = D38113.1 # NC_006492.4 = DP000054.3 printf "chrM\t0\t16554\tD38113.1\n" >> ucscToINSDC.bed printf "chrY\t0\t26350515\tNC_006492.4\n" >> ucscToINSDC.bed # resort the bed file: sort -k1,1 -k2,2n -o ucscToINSDC.bed ucscToINSDC.bed # verify chrM and chrY are correct: egrep "chrM|chrY" * ucscToINSDC.bed:chrM 0 16554 D38113.1 ucscToINSDC.bed:chrY 0 26350515 NC_006492.4 ucscToRefSeq.bed:chrM 0 16554 NC_001643.1 ucscToRefSeq.bed:chrY 0 26350515 NC_006492.4 # should be same line counts throughout: wc -l * ../../chrom.sizes # 4346 ucscToINSDC.bed # 4346 ucscToRefSeq.bed # 4346 ../../chrom.sizes export chrSize=`cut -f1 ucscToINSDC.bed | awk '{print length($0)}' | sort -n | tail -1` echo $chrSize # 27 # use the $chrSize in this sed sed -e "s/21/$chrSize/" $HOME/kent/src/hg/lib/ucscToINSDC.sql \ | hgLoadSqlTab panTro6 ucscToINSDC stdin ucscToINSDC.bed # should be the same for ucscToRefSeq: export chrSize=`cut -f1 ucscToRefSeq.bed | awk '{print length($0)}' | sort -n | tail -1` echo $chrSize # 27 sed -e "s/21/$chrSize/" $HOME/kent/src/hg/lib/ucscToINSDC.sql \ | sed -e 's/INSDC/RefSeq/g;' > ucscToRefSeq.sql hgLoadSqlTab panTro6 ucscToRefSeq ./ucscToRefSeq.sql ucscToRefSeq.bed # checkTableCoords should be silent checkTableCoords panTro6 # each should cover %100 entirely: featureBits -countGaps panTro6 ucscToINSDC # 3050398082 bases of 3050398082 (100.000%) in intersection featureBits -countGaps panTro6 ucscToRefSeq # 3050398082 bases of 3050398082 (100.000%) in intersection ######################################################################### # add chromAlias table (DONE - 2018-03-24 - Hiram) mkdir /hive/data/genomes/panTro6/bed/chromAlias cd /hive/data/genomes/panTro6/bed/chromAlias hgsql -N -e 'select chrom,name from ucscToRefSeq;' panTro6 \ | sort -k1,1 > ucsc.refseq.tab hgsql -N -e 'select chrom,name from ucscToINSDC;' panTro6 \ | sort -k1,1 > ucsc.genbank.tab ~/kent/src/hg/utils/automation/chromAlias.pl ucsc.*.tab \ > panTro6.chromAlias.tab for t in refseq genbank do c0=`cat ucsc.$t.tab | wc -l` c1=`grep $t panTro6.chromAlias.tab | wc -l` ok="OK" if [ "$c0" -ne "$c1" ]; then ok="ERROR" fi printf "# checking $t: $c0 =? $c1 $ok\n" done # checking refseq: 4346 =? 4346 OK # checking genbank: 4346 =? 4346 OK hgLoadSqlTab panTro6 chromAlias ~/kent/src/hg/lib/chromAlias.sql \ panTro6.chromAlias.tab ######################################################################### # fixup search rule for assembly track/gold table (DONE - 2018-03-24 - Hiram) cd ~/kent/src/hg/makeDb/trackDb/chimp/panTro6 # preview prefixes and suffixes: hgsql -N -e "select frag from gold;" panTro6 \ | sed -e 's/[0-9][0-9]*//;' | sort | uniq -c | sed -e 's/^/#\t/;' # 14 AACZ.1 # 21 AC.1 # 90 AC.2 # 53 AC.3 # 22 AC.4 # 11 AC.5 # 3 AC.6 # 2 BS.2 # 5037 NBAG.1 # 1 NC_.1 # implies a rule: '[ABN][ACSB][ACGZ0-9_]+(\.[0-9]+)?' # verify this rule will find them all and eliminate them all: hgsql -N -e "select frag from gold;" panTro6 | wc -l # 5254 hgsql -N -e "select frag from gold;" panTro6 \ | egrep -e '[ABN][ACSB][ACGZ0-9_]+(\.[0-9]+)?' | wc -l # 5254 hgsql -N -e "select frag from gold;" panTro6 \ | egrep -v -e '[ABN][ACSB][ACGZ0-9_]+(\.[0-9]+)?' | wc -l # 0 # hence, add to trackDb/chicken/panTro6/trackDb.ra searchTable gold shortCircuit 1 termRegex [ABN][ACSB][ACGZ0-9_]+(\.[0-9]+)? query select chrom,chromStart,chromEnd,frag from %s where frag like '%s%%' searchPriority 8 # verify searches work in the position box ############################################################################# # running repeat masker (DONE - 2018-03-24 - Hiram) mkdir /hive/data/genomes/panTro6/bed/repeatMasker cd /hive/data/genomes/panTro6/bed/repeatMasker time (doRepeatMasker.pl -buildDir=`pwd` \ -bigClusterHub=ku -dbHost=hgwdev -workhorse=hgwdev \ -smallClusterHub=ku panTro6) > do.log 2>&1 & # real 1035m8.587s cat faSize.rmsk.txt egrep "bases|Total|masked" faSize.rmsk.txt \ | fold -w 75 -s | sed -e 's/^/# /;' # 3050398082 bases (31805092 N's 3018592990 real 1405499360 upper 1613093630 # lower) in 4346 sequences in 1 files # Total size: mean 701886.4 sd 9434013.2 min 223 (chrUn_NW_019937062v1) max # 224244399 (chr1) median 29187 # %52.88 masked total, %53.44 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 panTro6 rmsk # 1613093500 bases of 3050398082 (52.881%) in intersection # real 0m35.581s # why is it different than the faSize above ? # because rmsk masks out some N's as well as bases, the faSize 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 on high contig count assemblies: time hgsql -N -e 'select genoName,genoStart,genoEnd from rmsk;' panTro6 \ | bedSingleCover.pl stdin | ave -col=4 stdin | grep "^total" # total 1613093500.000000 # real 0m38.395s ########################################################################## # running simple repeat (DONE - 2018-03-24 - Hiram) mkdir /hive/data/genomes/panTro6/bed/simpleRepeat cd /hive/data/genomes/panTro6/bed/simpleRepeat # using trf409 6 here as similar size to genome (human == 6) time (doSimpleRepeat.pl -buildDir=`pwd` -bigClusterHub=ku \ -dbHost=hgwdev -workhorse=hgwdev -smallClusterHub=ku \ -trf409 6 panTro6) > do.log 2>&1 & # real 273m49.147s cat fb.simpleRepeat # 222649611 bases of 3018592990 (7.376%) in intersection bigBedInfo *.bb | sed -e 's/^/# /;' # version: 4 # fieldCount: 16 # hasHeaderExtension: yes # isCompressed: yes # isSwapped: 0 # extraIndexCount: 0 # itemCount: 996,217 # primaryDataSize: 31,637,595 # primaryIndexSize: 202,580 # zoomLevels: 10 # chromCount: 4274 # basesCovered: 222,649,611 # meanDepth (of bases covered): 1.833462 # minDepth: 1.000000 # maxDepth: 88.000000 # std of depth: 2.284835 # adding this trfMask to the other masking cd /hive/data/genomes/panTro6 # when using the Window Masker result: # twoBitMask bed/windowMasker/panTro6.cleanWMSdust.2bit \ # -add bed/simpleRepeat/trfMask.bed panTro6.2bit # you can safely ignore the warning about fields >= 13 # when using Rmsk results, add to rmsk after it is done: twoBitMask panTro6.rmsk.2bit \ -add bed/simpleRepeat/trfMask.bed panTro6.2bit # you can safely ignore the warning about fields >= 13 twoBitToFa panTro6.2bit stdout | faSize stdin > faSize.panTro6.2bit.txt egrep "bases|Total|masked" faSize.panTro6.2bit.txt \ | fold -w 75 -s | sed -e 's/^/# /;' # 3050398082 bases (31805092 N's 3018592990 real 1402090427 upper 1616502563 # lower) in 4346 sequences in 1 files # Total size: mean 701886.4 sd 9434013.2 min 223 (chrUn_NW_019937062v1) max # 224244399 (chr1) median 29187 # %52.99 masked total, %53.55 masked real # reset the symlink rm /gbdb/panTro6/panTro6.2bit ln -s `pwd`/panTro6.2bit /gbdb/panTro6/panTro6.2bit ######################################################################### # CREATE MICROSAT TRACK (DONE - 2018-03-24 - Hiram) ssh hgwdev mkdir /cluster/data/panTro6/bed/microsat cd /cluster/data/panTro6/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 panTro6 microsat microsat.bed # Read 28577 elements of size 4 from microsat.bed ########################################################################## ## WINDOWMASKER (DONE - 2018-03-24 - Hiram) mkdir /hive/data/genomes/panTro6/bed/windowMasker cd /hive/data/genomes/panTro6/bed/windowMasker time (doWindowMasker.pl -buildDir=`pwd` -workhorse=hgwdev \ -dbHost=hgwdev panTro6) > do.log 2>&1 # real 188m5.912s # Masking statistics cat faSize.panTro6.cleanWMSdust.txt egrep "bases|Total|masked" faSize.panTro6.cleanWMSdust.txt \ | fold -w 75 -s | sed -e 's/^/# /;' # 3050398082 bases (31805092 N's 3018592990 real 1812556664 upper 1206036326 # lower) in 4346 sequences in 1 files # Total size: mean 701886.4 sd 9434013.2 min 223 (chrUn_NW_019937062v1) max # 224244399 (chr1) median 29187 # %39.54 masked total, %39.95 masked real cat fb.panTro6.rmsk.windowmaskerSdust.txt # 971547886 bases of 3050398082 (31.850%) in intersection ############################################################################# # ncbiRefSeq (DONE - 2018-03-24 - Hiram) # can be run up after ucscToRefSeq table is constructed mkdir /hive/data/genomes/panTro6/bed/ncbiRefSeq cd /hive/data/genomes/panTro6/bed/ncbiRefSeq # adjust the name arguments time (~/kent/src/hg/utils/automation/doNcbiRefSeq.pl -buildDir=`pwd` \ -bigClusterHub=ku -dbHost=hgwdev \ -fileServer=hgwdev -smallClusterHub=ku -workhorse=hgwdev \ refseq vertebrate_mammalian Pan_troglodytes \ GCF_002880755.1_Clint_PTRv2 panTro6) > do.log 2>&1 # real 10m2.131s # started this too early. It needs to run after the panTro6.2bit file # has been masked. Rerunning from process step: time (~/kent/src/hg/utils/automation/doNcbiRefSeq.pl -buildDir=`pwd` \ -continue=process -bigClusterHub=ku -dbHost=hgwdev \ -fileServer=hgwdev -smallClusterHub=ku -workhorse=hgwdev \ refseq vertebrate_mammalian Pan_troglodytes \ GCF_002880755.1_Clint_PTRv2 panTro6) > process.log 2>&1 & # real 8m52.047s cat fb.ncbiRefSeq.panTro6.txt # 81659062 bases of 2476453204 (3.297%) in intersection ############################################################################# # cpgIslands - (DONE - 2018-03-24 - Hiram) mkdir /hive/data/genomes/panTro6/bed/cpgIslands cd /hive/data/genomes/panTro6/bed/cpgIslands time (doCpgIslands.pl -dbHost=hgwdev -bigClusterHub=ku \ -workhorse=hgwdev -smallClusterHub=ku panTro6) > do.log 2>&1 & # real 5m35.611s cat fb.panTro6.cpgIslandExt.txt # 22143193 bases of 3018592990 (0.734%) in intersection ############################################################################## # genscan - (DONE - 2018-03-24 - Hiram) mkdir /hive/data/genomes/panTro6/bed/genscan cd /hive/data/genomes/panTro6/bed/genscan time (doGenscan.pl -buildDir=`pwd` -workhorse=hgwdev -dbHost=hgwdev \ -bigClusterHub=ku panTro6) > do.log 2>&1 & # real 182m50.882s cat fb.panTro6.genscan.txt # 53595000 bases of 3018592990 (1.775%) in intersection cat fb.panTro6.genscanSubopt.txt # 51298399 bases of 3018592990 (1.699%) in intersection bigBedInfo panTro6.genscan.bb | sed -e 's/^/# /;' # version: 4 # fieldCount: 12 # hasHeaderExtension: yes # isCompressed: yes # isSwapped: 0 # extraIndexCount: 0 # itemCount: 41,507 # primaryDataSize: 2,449,724 # primaryIndexSize: 38,244 # zoomLevels: 8 # chromCount: 871 # basesCovered: 1,998,870,176 # meanDepth (of bases covered): 1.000000 # minDepth: 1.000000 # maxDepth: 1.000000 # std of depth: 0.000000 ############################################################################# # augustus gene track (DONE - 2018-03-24 - Hiram) mkdir /hive/data/genomes/panTro6/bed/augustus cd /hive/data/genomes/panTro6/bed/augustus time (doAugustus.pl -buildDir=`pwd` -bigClusterHub=ku \ -species=human -dbHost=hgwdev -workhorse=hgwdev panTro6) > do.log 2>&1 & # real 98m3.215s cat fb.panTro6.augustusGene.txt # 50421577 bases of 3018592990 (1.670%) in intersection bigBedInfo panTro6.augustus.bb | sed -e 's/^/# /;' # version: 4 # fieldCount: 20 # hasHeaderExtension: yes # isCompressed: yes # isSwapped: 0 # extraIndexCount: 0 # itemCount: 30,411 # primaryDataSize: 2,164,577 # primaryIndexSize: 28,960 # zoomLevels: 7 # chromCount: 495 # basesCovered: 1,295,044,049 # meanDepth (of bases covered): 1.295008 # minDepth: 1.000000 # maxDepth: 4.000000 # std of depth: 0.662334 ############################################################################# # lastz/chain/net swap human/hg38 (DONE - 2018-03-24 - Hiram) # original alignment cd /hive/data/genomes/hg38/bed/lastzPanTro6.2018-03-24 cat fb.hg38.chainPanTro6Link.txt # 2910625246 bases of 3049335806 (95.451%) in intersection cat fb.hg38.chainSynPanTro6Link.txt # 2890994068 bases of 3049335806 (94.807%) in intersection cat fb.hg38.chainRBestPanTro6Link.txt # 2743876160 bases of 3049335806 (89.983%) in intersection # running the swap mkdir /hive/data/genomes/panTro6/bed/blastz.hg38.swap cd /hive/data/genomes/panTro6/bed/blastz.hg38.swap time (doBlastzChainNet.pl -verbose=2 \ -swap /hive/data/genomes/hg38/bed/lastzPanTro6.2018-03-24/DEF \ -chainMinScore=5000 -chainLinearGap=medium \ -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \ -syntenicNet) > swap.log 2>&1 # real 101m29.782s cat fb.panTro6.chainHg38Link.txt # 2814507414 bases of 3018592990 (93.239%) in intersection cat fb.panTro6.chainSynHg38Link.txt # 2800642800 bases of 3018592990 (92.780%) in intersection time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \ panTro6 hg38) > rbest.log 2>&1 & # real 102m47.533s cat fb.panTro6.chainRBestHg38Link.txt # 2748571185 bases of 3018592990 (91.055%) in intersection ############################################################################# # lastz/chain/net swap mouse/mm10 (DONE - 2018-03-24 - Hiram) # alignment to mouse/mm10: cd /hive/data/genomes/mm10/bed/lastzPanTro6.2018-03-24/ cat fb.mm10.chainPanTro6Link.txt # 935720585 bases of 2652783500 (35.273%) in intersection cat fb.mm10.chainRBestPanTro6Link.txt # 891553355 bases of 2652783500 (33.608%) in intersection # and for the swap: mkdir /hive/data/genomes/panTro6/bed/blastz.mm10.swap cd /hive/data/genomes/panTro6/bed/blastz.mm10.swap time (doBlastzChainNet.pl -verbose=2 \ /hive/data/genomes/mm10/bed/lastzPanTro6.2018-03-24/DEF \ -swap -chainMinScore=3000 -chainLinearGap=medium \ -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \ -syntenicNet) > swap.log 2>&1 # real 78m57.631s cat fb.panTro6.chainMm10Link.txt # 934668641 bases of 3018592990 (30.964%) in intersection cat fb.panTro6.chainSynMm10Link.txt # 889944141 bases of 3018592990 (29.482%) in intersection time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \ panTro6 mm10) > rbest.log 2>&1 & # real 504m47.811s cat fb.panTro6.chainRBestMm10Link.txt # 890065520 bases of 3018592990 (29.486%) in intersection ############################################################################## # Create kluster run files (DONE - 2018-03-24 - Hiram) cd /hive/data/genomes/panTro6 # numerator is panTro6 gapless bases "real" as reported by: featureBits -noRandom -noHap panTro6 gap # 28994139 bases of 2803637675 (1.034%) 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 \( 2803637675 / 2861349177 \) \* 1024 # ( 2803637675 / 2861349177 ) * 1024 = 1003.346604 # ==> use -repMatch=1000 same as was panTro5 cd /hive/data/genomes/panTro6 blat panTro6.2bit \ /dev/null /dev/null -tileSize=11 -makeOoc=jkStuff/panTro6.11.ooc \ -repMatch=1000 # Wrote 36740 overused 11-mers to jkStuff/panTro6.11.ooc # panTro5 at repMatch=1000 was: # Wrote 38245 overused 11-mers to jkStuff/panTro5.11.ooc # check non-bridged gaps to see what the typical size is: hgsql -N \ -e 'select * from gap where bridge="no" order by size;' panTro6 \ | sort -k7,7nr | ave -col=7 stdin | sed -e 's/^/# /;' # there are many at 100 bases: # Q1 100.000000 # median 100.000000 # Q3 100.000000 # average 10930.290698 # min 10.000000 # max 500001.000000 # count 86 # total 940005.000000 # standard deviation 56419.602180 # profile: hgsql -N -e 'select * from gap where bridge="no" order by size;' panTro6 \ | cut -f7 | sort | uniq -c 1 10 74 100 1 10223 1 131931 1 15585 1 29588 1 32403 1 33521 1 500001 2 50001 1 70431 1 8910 # therefore, minimum gap size of 100, this is doing non-bridged gaps only gapToLift -verbose=2 -minGap=100 panTro6 jkStuff/panTro6.nonBridged.lft \ -bedFile=stdout | sort -k1,1 -k2,2n > jkStuff/panTro6.nonBridged.bed ############################################################################## # LIFTOVER TO panTro5 (DONE - 2018-03-24 - Hiram) ssh hgwdev mkdir /hive/data/genomes/panTro6/bed/blat.panTro5.2018-03-24 cd /hive/data/genomes/panTro6/bed/blat.panTro5.2018-03-24 time (doSameSpeciesLiftOver.pl -verbose=2 -buildDir=`pwd` \ -ooc=/hive/data/genomes/panTro6/jkStuff/panTro6.11.ooc \ -bigClusterHub=ku -dbHost=hgwdev -workhorse=hgwdev \ panTro6 panTro5) > do.log 2>&1 # real 464m42.018s # verify the convert link on the test browser is now active from panTro6 to # panTro5 ############################################################################## # GENBANK AUTO UPDATE (DONE - 2018-03-25 - Hiram) ssh hgwdev cd $HOME/kent/src/hg/makeDb/genbank git pull # /cluster/data/genbank/data/organism.lst shows: # #organism mrnaCnt estCnt refSeqCnt # Pan troglodytes 3548 5065 2048 # Pan troglodytes schweinfurthii 7 0 0 # Pan troglodytes troglodytes 42 0 0 # Pan troglodytes verus 126 12315 0 # edit etc/genbank.conf to add panTro6 just before panTro5 # panTro6 (chimp - Pan troglodytes - refseq GCF_002880755.1 - taxId 9598) panTro6.serverGenome = /hive/data/genomes/panTro6/panTro6.2bit panTro6.clusterGenome = /hive/data/genomes/panTro6/panTro6.2bit panTro6.ooc = /hive/data/genomes/panTro6/jkStuff/panTro6.11.ooc panTro6.lift = /hive/data/genomes/panTro6/jkStuff/panTro6.nonBridged.lft panTro6.perChromTables = no panTro6.refseq.mrna.native.pslCDnaFilter = ${finished.refseq.mrna.native.pslCDnaFilter} panTro6.refseq.mrna.xeno.pslCDnaFilter = ${finished.refseq.mrna.xeno.pslCDnaFilter} panTro6.genbank.mrna.native.pslCDnaFilter = ${finished.genbank.mrna.native.pslCDnaFilter} panTro6.genbank.mrna.xeno.pslCDnaFilter = ${finished.genbank.mrna.xeno.pslCDnaFilter} panTro6.genbank.est.native.pslCDnaFilter = ${finished.genbank.est.native.pslCDnaFilter} panTro6.genbank.est.xeno.pslCDnaFilter = ${finished.genbank.est.xeno.pslCDnaFilter} panTro6.downloadDir = panTro6 # defaults yes: genbank.mrna.native.load genbank.mrna.native.loadDesc # yes: genbank.est.native.load refseq.mrna.native.load # yes: refseq.mrna.native.loadDesc refseq.mrna.xeno.load # yes: refseq.mrna.xeno.loadDesc # defaults no: genbank.mrna.xeno.load genbank.mrna.xeno.loadDesc # no: genbank.est.native.loadDesc genbank.est.xeno.load # no: genbank.est.xeno.loadDesc # DO NOT NEED genbank.mrna.xeno except for human, mouse # have been doing this for chimp too: panTro6.genbank.mrna.xeno.load = yes # verify stated file paths do exist: grep panTro6 etc/genbank.conf | egrep "Genome|ooc|lift" \ | awk '{print $NF}' | xargs ls -og -rw-rw-r-- 1 146968 Mar 24 20:30 /hive/data/genomes/panTro6/jkStuff/panTro6.11.ooc -rw-rw-r-- 1 258184 Mar 25 14:25 /hive/data/genomes/panTro6/jkStuff/panTro6.nonBridged.lft -rw-rw-r-- 1 795113145 Mar 24 20:22 /hive/data/genomes/panTro6/panTro6.2bit -rw-rw-r-- 1 795113145 Mar 24 20:22 /hive/data/genomes/panTro6/panTro6.2bit # add panTro6 to: # etc/align.dbs etc/hgwdev.dbs git commit -m 'adding panTro6/cat refs #21043' \ etc/genbank.conf etc/align.dbs etc/hgwdev.dbs git push # update /cluster/data/genbank/: make etc-update # XXX a few days later the genbank tables will be in the database ############################################################################# # BLATSERVERS ENTRY (DONE - 2018-08-26 - 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 ("panTro6", "blat1c", "17904", "1", "0"); \ INSERT INTO blatServers (db, host, port, isTrans, canPcr) \ VALUES ("panTro6", "blat1c", "17905", "0", "1");' \ hgcentraltest # test it with some sequence ############################################################################## ## reset default position to same as what panTro5 has: FOXP2 ## (DONE - 2018-04-09 - Hiram) ssh hgwdev hgsql -e 'update dbDb set defaultPos="chr7:111311998-111585728" where name="panTro6";' hgcentraltest ############################################################################## # all.joiner update, downloads and in pushQ - (DONE - 2018-04-09 - Hiram) cd $HOME/kent/src/hg/makeDb/schema ~/kent/src/hg/utils/automation/verifyBrowser.pl panTro6 # 66 tables in database panTro6 - Chimp, Pan troglodytes # verified 66 tables in database panTro6, 0 extra tables, 24 optional tables # NCBI RefSeq genes 10 optional tables # chainNetRBestHg38 3 optional tables # chainNetRBestMm10 3 optional tables # chainNetSynHg38 3 optional tables # chainNetSynMm10 3 optional tables # gapOverlap 1 optional tables # tandemDups 1 optional tables # 13 genbank tables found # verified 29 required tables, 0 missing tables # hg38 chainNet to panTro6 found 3 required tables # mm10 chainNet to panTro6 found 3 required tables # hg38 chainNet RBest and syntenic to panTro6 found 6 optional tables # mm10 chainNet RBest and syntenic to panTro6 found 3 optional tables # liftOver to previous versions: 1, from previous versions: 1 # fixup all.joiner until this is a clean output joinerCheck -database=panTro6 -tableCoverage all.joiner joinerCheck -database=panTro6 -times all.joiner joinerCheck -database=panTro6 -keys all.joiner cd /hive/data/genomes/panTro6 # clean up obsolete trackDb work, assuming you have already checked in # these trackDb files into the source tree rm -fr TemporaryTrackDbCheckout time (makeDownloads.pl -workhorse=hgwdev panTro6) > downloads.log 2>&1 # real 25m49.888s # now ready for pushQ entry mkdir /hive/data/genomes/panTro6/pushQ cd /hive/data/genomes/panTro6/pushQ time (makePushQSql.pl -redmineList panTro6) > panTro6.pushQ.sql 2> stderr.out # remove the tandemDups and gapOverlap from the file list: sed -i -e "/tandemDups/d" redmine.panTro6.table.list sed -i -e "/Tandem Dups/d" redmine.panTro6.releaseLog.txt sed -i -e "/gapOverlap/d" redmine.panTro6.table.list sed -i -e "/Gap Overlaps/d" redmine.panTro6.releaseLog.txt # check for errors in stderr.out, some are OK, e.g.: # WARNING: panTro6 does not have seq # WARNING: panTro6 does not have extFile # add the path names to the listing files in the redmine issue # in the three appropriate entry boxes: /hive/data/genomes/panTro6/pushQ/redmine.panTro6.file.list /hive/data/genomes/panTro6/pushQ/redmine.panTro6.releaseLog.txt /hive/data/genomes/panTro6/pushQ/redmine.panTro6.table.list #########################################################################