# for emacs: -*- mode: sh; -*- # This file describes browser build for the micMur3 ######################################################################### # photograph obtained for micMur1 (DONE - 2009-08-04 - Hiram) From: http://pin.primate.wisc.edu/fs/sheets/images/623lg.jpg checked into the source tree cd /hive/data/genomes/micMur3 # establish photoReference.txt printf 'photoCreditURL\thttp://pin.primate.wisc.edu/factsheets/image/623 photoCreditName\tVerena Behringer, Primate Info Net\n' > photoReference.txt ######################################################################### # Initial steps (DONE - 2017-03-02 - Hiram) # To start this initialBuild.txt document, from a previous assembly document: mkdir ~/kent/src/hg/makeDb/doc/micMur3 cd ~/kent/src/hg/makeDb/doc/micMur3 # best to use a most recent document since it has the latest features and # procedures: sed -e 's/rhiBie1/micMur3/g; s/RhiBie1/MicMur3/g; s/DONE/TBD/g;' \ ../rhiBie1/initialBuild.txt > initialBuild.txt mkdir /hive/data/genomes/micMur3/refseq cd /hive/data/genomes/micMur3/refseq rsync -L -a -P \ rsync://ftp.ncbi.nlm.nih.gov/genomes/refseq/vertebrate_mammalian/Microcebus_murinus/all_assembly_versions/GCF_000165445.2_Mmur_3.0/ ./ # sent 4721 bytes received 3531529625 bytes 16697561.92 bytes/sec # total size is 3531081508 speedup is 1.00 # real 3m31.809s # check assembly size for later reference: faSize G*3.0_genomic.fna.gz # 2487409138 bases (101087241 N's 2386321897 real 1655405674 upper # 730916223 lower) in 7678 sequences in 1 files # Total size: mean 323965.8 sd 5602567.1 min 60 (NW_017971431.1) # max 159902609 (NC_033667.1) median 3315 # %29.38 masked total, %30.63 masked real # this information is from the top of # micMur3/refseq/GCF_000165445.2_Mmur_3.0_assembly_report.txt # Assembly name: Mmur_3.0 # Organism name: Microcebus murinus (gray mouse lemur) # Isolate: mixed # Sex: pooled male and female # Taxid: 30608 # BioSample: SAMN06275470 # BioProject: PRJNA19967 # Submitter: Broad Institute # Date: 2017-2-6 # Assembly type: haploid # Release type: major # Assembly level: Chromosome # Genome representation: full # WGS project: ABDC03 # Assembly method: AllPathsLG v. 41070; Atlas Link v. 1.0; Atlas GapFill v. 2.0; PBJelly2 v. 14.9.9; Lachesis v. shendurelab-LACHESIS-2151de9; BioNano IrysSolve v. 2.1 # Genome coverage: 221.6x # Sequencing technology: Illumina; PacBio RS; PacBio RSII # RefSeq category: Representative Genome # GenBank assembly accession: GCA_000165445.3 # RefSeq assembly accession: GCF_000165445.2 # RefSeq assembly and GenBank assemblies identical: no # ## Assembly-Units: ## GenBank Unit Accession RefSeq Unit Accession Assembly-Unit name ## GCA_000165455.3 GCF_000165455.2 Primary Assembly ## GCF_001995325.1 non-nuclear ############################################################################# # establish config.ra file (DONE - Hiram - 2017-03-02) # arguments here are: cd /hive/data/genomes/micMur3 $HOME/kent/src/hg/utils/automation/prepConfig.pl micMur3 mammal \ mouseLemur ./refseq/*_assembly_report.txt > micMur3.config.ra # verify it looks sane cat micMur3.config.ra # config parameters for makeGenomeDb.pl: db micMur3 clade mammal genomeCladePriority 35 scientificName Microcebus murinus commonName Gray mouse lemur assemblyDate Feb. 2017 assemblyLabel Broad Institute assemblyShortLabel Mmur_3.0 orderKey 7727 # mitochondrial sequence included in refseq release # mitoAcc NC_028718.1 mitoAcc none fastaFiles /hive/data/genomes/micMur3/ucsc/*.fa.gz agpFiles /hive/data/genomes/micMur3/ucsc/*.agp # qualFiles none dbDbSpeciesDir mouseLemur photoCreditURL http://pin.primate.wisc.edu/factsheets/image/623 photoCreditName Verena Behringer, Primate Info Net ncbiGenomeId 777 ncbiAssemblyId 998221 ncbiAssemblyName Mmur_3.0 ncbiBioProject 19967 ncbiBioSample SAMN06275470 genBankAccessionID GCF_000165445.2 taxId 30608 ############################################################################# # setup UCSC named files (DONE - 2017-03-02 - Hiram) mkdir /hive/data/genomes/micMur3/ucsc cd /hive/data/genomes/micMur3/ucsc # check for duplicate sequences: time faToTwoBit -noMask ../refseq/G*3.0_genomic.fna.gz refseq.2bit # real 1m5.656s 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 ~/kent/src/hg/utils/automation/ucscCompositeAgp.pl \ ../refseq/G*3.0_genomic.fna.gz \ ../refseq/G*3.0_assembly_structure/Primary_Assembly # NC_033660.1 chr1 # NC_033661.1 chr2 # NC_033662.1 chr3 ... etc ... # NC_033690.1 chr31 # NC_033691.1 chr32 # NC_033692.1 chrX time ~/kent/src/hg/utils/automation/unplacedWithChroms.pl \ ../refseq/*_assembly_structure/Primary_Assembly # processed 2913 sequences into chrUn.fa.gz # real 0m48.790s time ~/kent/src/hg/utils/automation/unlocalizedWithChroms.pl \ ../refseq/*_assembly_structure/Primary_Assembly # 11 # 7 # 17 # 22 # 1 # 18 # 30 # 23 # 16 # 13 # 29 # 27 # 25 # X # 3 # 9 # 12 # 20 # 14 # 15 # 4 # 10 # 19 # 31 # 5 # processed 4731 sequences into chr*_random.gz 25 files # real 1m2.176s # bash syntax here mitoAcc=`grep "^# mitoAcc" ../micMur3.config.ra | awk '{print $NF}'` printf "# mitoAcc %s\n" "$mitoAcc" # mitoAcc NC_028718.1 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 1m13.235s time cat *.agp | checkAgpAndFa stdin test.2bit 2>&1 | tail -4 # All AGP and FASTA entries agree - both files are valid # real 0m14.336s # and no sequence lost from orginal: # (well except for the one dropped contig) twoBitToFa test.2bit stdout | faSize stdin # 2487409138 bases (101087241 N's 2386321897 real 2386321897 upper 0 lower) # in 7678 sequences in 1 files # Total size: mean 323965.8 sd 5602567.1 min 60 (chrUn_NW_017971431v1) # max 159902609 (chr8) median 3315 # same numbers as above # 2487409138 bases (101087241 N's 2386321897 real 1655405674 upper # 730916223 lower) in 7678 sequences in 1 files # Total size: mean 323965.8 sd 5602567.1 min 60 (NW_017971431.1) # max 159902609 (NC_033667.1) median 3315 # no longer need these temporary 2bit files rm refseq.2bit test.2bit ############################################################################# # Initial database build (DONE - 2017-03-02 - Hiram) cd /hive/data/genomes/micMur3 # verify sequence and AGP are OK: time (makeGenomeDb.pl -workhorse=hgwdev -dbHost=hgwdev -fileServer=hgwdev \ -stop=agp micMur3.config.ra) > agp.log 2>&1 # real 2m49.535s # then finish it off: time (makeGenomeDb.pl -workhorse=hgwdev -dbHost=hgwdev \ -fileServer=hgwdev -continue=db micMur3.config.ra) > db.log 2>&1 # real 21m19.801s # check in the trackDb files created in TemporaryTrackDbCheckout/ # and add micMur3 to trackDb/makefile # temporary symlink until masked sequence is available cd /hive/data/genomes/micMur3 ln -s `pwd`/micMur3.unmasked.2bit /gbdb/micMur3/micMur3.2bit ############################################################################## # cpgIslands on UNMASKED sequence (DONE - 2017-03-02 - Hiram) mkdir /hive/data/genomes/micMur3/bed/cpgIslandsUnmasked cd /hive/data/genomes/micMur3/bed/cpgIslandsUnmasked time (doCpgIslands.pl -dbHost=hgwdev -bigClusterHub=ku -buildDir=`pwd` \ -tableName=cpgIslandExtUnmasked \ -maskedSeq=/hive/data/genomes/micMur3/micMur3.unmasked.2bit \ -workhorse=hgwdev -smallClusterHub=ku micMur3) > do.log 2>&1 # real 7m9.382s cat fb.micMur3.cpgIslandExtUnmasked.txt # 63732015 bases of 2386321975 (2.671%) in intersection ############################################################################# # cytoBandIdeo - (DONE - 2017-03-02 - Hiram) mkdir /hive/data/genomes/micMur3/bed/cytoBand cd /hive/data/genomes/micMur3/bed/cytoBand makeCytoBandIdeo.csh micMur3 ######################################################################### # ucscToINSDC and ucscToRefSeq table/track (DONE - 2017-03-02 - 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/micMur3/bed/ucscToINSDC cd /hive/data/genomes/micMur3/bed/ucscToINSDC # find accession for chrM grep chrM ../../micMur3.agp # chrM 1 17114 1 O NC_028718.1 1 17114 + # find the genbank accession for NC_026976.1 at Entrez nucleotide # The NC_028718.1 name is the RefSeq name, the genbank name is: KR911908.1 # the assembly_report does not have this KP name since the chrM sequence # is not in the genbank assembly: grep NC_028718.1 ../../refseq/GCF*3.0_assembly_report.txt # MT assembled-molecule MT Mitochondrion na <> NC_028718.1 non-nuclear 17114 na # if there is a chrM, use its INSDC name as a second argument: # this is a RefSeq assembly, use the chrM refSeq name: ~/kent/src/hg/utils/automation/ucscToINSDC.sh \ ../../refseq/GCF_*structure/Primary_Assembly NC_028718.1 # this is actually ucscToRefSeq since this is a RefSeq assembly sort -k2 ucscToINSDC.txt > ucscToRefSeq.txt awk '{printf "%s\t%s\n", $2, $1}' ucscToRefSeq.txt \ | sort > refSeqToUcsc.txt # chrM processing needs special help, fixup with the sed # extract the refseq vs. genbank names from the assembly_report # columns 5 and 7 are the INSDC and RefSeq names grep -v "^#" ../../refseq/GCF*_assembly_report.txt | cut -f5,7 \ | awk '{printf "%s\t%s\n", $2, $1}' | sed -e 's/na/KR911908.1/' \ | sort > refseq.insdc.txt awk '{printf "%s\t0\t%d\n", $1,$2}' ../../chrom.sizes \ | sort > ucsc.coordinate.tab join -2 2 refseq.insdc.txt ucscToRefSeq.txt | tr '[ ]' '[\t]' | sort -k3 \ | join -2 3 ucsc.coordinate.tab - | tr '[ ]' '[\t]' | cut -f1-4 \ > ucscToRefSeq.bed join -2 2 refseq.insdc.txt ucscToRefSeq.txt | tr '[ ]' '[\t]' | sort -k3 \ | join -2 3 ucsc.coordinate.tab - | tr '[ ]' '[\t]' | cut -f1-3,5 \ > ucscToINSDC.bed # verify chrM is correct: grep chrM *.bed # ucscToINSDC.bed:chrM 0 17114 KR911908.1 # ucscToRefSeq.bed:chrM 0 17114 NC_028718.1 # should be same line counts throughout: # in this case one is missing in the final result due to the duplicate # contig being removed wc -l * # 7678 refSeqToUcsc.txt # 7678 refseq.insdc.txt # 7678 ucsc.coordinate.tab # 7678 ucscToINSDC.bed # 7678 ucscToINSDC.txt # 7678 ucscToRefSeq.bed # 7678 ucscToRefSeq.txt cut -f1 ucscToINSDC.bed | awk '{print length($0)}' | sort -n | tail -1 # 25 # use the 25 in this sed sed -e "s/21/25/" $HOME/kent/src/hg/lib/ucscToINSDC.sql \ | hgLoadSqlTab micMur3 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 micMur3 ucscToRefSeq ./ucscToRefSeq.sql ucscToRefSeq.bed # checkTableCoords should be silent checkTableCoords micMur3 # each should cover %100 entirely: featureBits -countGaps micMur3 ucscToINSDC # 2487409138 bases of 2487409138 (100.000%) in intersection featureBits -countGaps micMur3 ucscToRefSeq # 2487409138 bases of 2487409138 (100.000%) in intersection ######################################################################### # add chromAlias table (DONE - 2017-03-02 - Hiram) mkdir /hive/data/genomes/micMur3/bed/chromAlias cd /hive/data/genomes/micMur3/bed/chromAlias hgsql -N -e 'select chrom,name,"refseq" from ucscToRefSeq;' micMur3 \ > ucsc.refseq.tab hgsql -N -e 'select chrom,name,"genbank" from ucscToINSDC;' micMur3 \ > ucsc.genbank.tab awk '{printf "%s\t%s\t%s\n", $2,$1,$3}' ucsc.genbank.tab ucsc.refseq.tab \ | sort > micMur3.chromAlias.tab hgLoadSqlTab micMur3 chromAlias ~/kent/src/hg/lib/chromAlias.sql \ micMur3.chromAlias.tab cd /hive/data/genomes/micMur3/bed/chromAlias # add ensembl names 2017-12-14 mkdir previous mv *.tab previous join -t$'\t' ../idKeys/micMur3.idKeys.txt \ ../../ensembl/ensemblMicMur3.idKeys.txt \ | cut -f2,3 | sort > ucsc.ensembl.tab cut -f1,2 previous/ucsc.refseq.tab > ucsc.refseq.tab cut -f1,2 previous/ucsc.genbank.tab > ucsc.genbank.tab ~/kent/src/hg/utils/automation/chromAlias.pl sort -o micMur3.chromAlias.tab micMur3.chromAlias.tab for t in refseq genbank ensembl do c0=`cat ucsc.$t.tab | wc -l` c1=`grep $t micMur3.chromAlias.tab | wc -l` ok="OK" if [ "$c0" -ne "$c1" ]; then ok="ERROR" fi printf "# checking $t: $c0 =? $c1 $ok\n" done # checking refseq: 7678 =? 7678 OK # checking genbank: 7678 =? 7678 OK # checking ensembl: 7678 =? 7678 OK hgLoadSqlTab micMur3 chromAlias ~/kent/src/hg/lib/chromAlias.sql \ micMur3.chromAlias.tab ######################################################################### # fixup search rule for assembly track/gold table (DONE - 2017-03-02 - Hiram) cd ~/kent/src/hg/makeDb/trackDb/mouseLemur/micMur3 # preview prefixes and suffixes: hgsql -N -e "select frag from gold;" micMur3 \ | sed -e 's/[0-9][0-9]*//;' | sort | uniq -c 50982 ABDC.1 1 NC_.1 # implies a rule: '[AN][BC][D_][C0-9]+(\.[0-9]+)?' # verify this rule will find them all and eliminate them all: hgsql -N -e "select frag from gold;" micMur3 | wc -l # 50983 hgsql -N -e "select frag from gold;" micMur3 \ | egrep -e '[AN][BC][D_][C0-9]+(\.[0-9]+)?' | wc -l # 50983 hgsql -N -e "select frag from gold;" micMur3 \ | egrep -v -e '[AN][BC][D_][C0-9]+(\.[0-9]+)?' | wc -l # 0 # hence, add to trackDb/chicken/micMur3/trackDb.ra searchTable gold shortCircuit 1 termRegex [AN][BC][D_][C0-9]+(\.[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 - 2017-03-02 - Hiram) mkdir /hive/data/genomes/micMur3/bed/repeatMasker cd /hive/data/genomes/micMur3/bed/repeatMasker time (doRepeatMasker.pl -buildDir=`pwd` \ -bigClusterHub=ku -dbHost=hgwdev -workhorse=hgwdev \ -smallClusterHub=ku micMur3) > do.log 2>&1 # real 603m18.086s cat faSize.rmsk.txt # 2487409138 bases (101087241 N's 2386321897 real 1403005122 upper # 983316775 lower) in 7678 sequences in 1 files # Total size: mean 323965.8 sd 5602567.1 min 60 (chrUn_NW_017971431v1) # max 159902609 (chr8) median 3315 # %39.53 masked total, %41.21 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 micMur3 rmsk # 983557115 bases of 2487409138 (39.541%) in intersection # real 0m40.666s # 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;' micMur3 \ | bedSingleCover.pl stdin | ave -col=4 stdin | grep "^total" # total 983557115.000000 # real 0m29.004s ########################################################################## # running simple repeat (DONE - 2017-03-02 - Hiram) mkdir /hive/data/genomes/micMur3/bed/simpleRepeat cd /hive/data/genomes/micMur3/bed/simpleRepeat # using trf409 3 here guessing smaller genome (human == 6) time (doSimpleRepeat.pl -buildDir=`pwd` -bigClusterHub=ku \ -dbHost=hgwdev -workhorse=hgwdev -smallClusterHub=ku \ -trf409 6 micMur3) > do.log 2>&1 # real 9m56.837s cat fb.simpleRepeat # 36504869 bases of 2386321975 (1.530%) in intersection # adding this trfMask to the other masking cd /hive/data/genomes/micMur3 # when using the Window Masker result: # twoBitMask bed/windowMasker/micMur3.cleanWMSdust.2bit \ # -add bed/simpleRepeat/trfMask.bed micMur3.2bit # you can safely ignore the warning about fields >= 13 # when using Rmsk results, add to rmsk after it is done: twoBitMask micMur3.rmsk.2bit \ -add bed/simpleRepeat/trfMask.bed micMur3.2bit # you can safely ignore the warning about fields >= 13 twoBitToFa micMur3.2bit stdout | faSize stdin > faSize.micMur3.2bit.txt cat faSize.micMur3.2bit.txt # 2487409138 bases (101087241 N's 2386321897 real 1401452057 upper # 984869840 lower) in 7678 sequences in 1 files # Total size: mean 323965.8 sd 5602567.1 min 60 (chrUn_NW_017971431v1) # max 159902609 (chr8) median 3315 # %39.59 masked total, %41.27 masked real # reset the symlink rm /gbdb/micMur3/micMur3.2bit ln -s `pwd`/micMur3.2bit /gbdb/micMur3/micMur3.2bit ######################################################################### # CREATE MICROSAT TRACK (DONE - 2017-03-02 - Hiram) ssh hgwdev mkdir /cluster/data/micMur3/bed/microsat cd /cluster/data/micMur3/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 micMur3 microsat microsat.bed # Read 28013 elements of size 4 from microsat.bed ########################################################################## ## WINDOWMASKER (DONE - 2017-03-03 - Hiram) mkdir /hive/data/genomes/micMur3/bed/windowMasker cd /hive/data/genomes/micMur3/bed/windowMasker time (doWindowMasker.pl -buildDir=`pwd` -workhorse=hgwdev \ -dbHost=hgwdev micMur3) > do.log 2>&1 # real 177m39.332s # Masking statistics cat faSize.micMur3.cleanWMSdust.txt # 2487409138 bases (101087241 N's 2386321897 real 1638833772 upper # 747488125 lower) in 7678 sequences in 1 files # Total size: mean 323965.8 sd 5602567.1 min 60 (chrUn_NW_017971431v1) # max 159902609 (chr8) median 3315 # %30.05 masked total, %31.32 masked real cat fb.micMur3.rmsk.windowmaskerSdust.txt # 474901533 bases of 2487409138 (19.092%) in intersection ########################################################################## # run up idKeys files for ncbiRefSeq (DONE - 2017-03-03 - Hiram) mkdir /hive/data/genomes/micMur3/bed/idKeys cd /hive/data/genomes/micMur3/bed/idKeys time (doIdKeys.pl -buildDir=`pwd` micMur3) > do.log 2>&1 & # real 180m9.149s cat micMur3.keySignature.txt # 591eccd7f439191e0ef7dcd523963ffb ########################################################################## # cpgIslands - (DONE - 2017-03-03 - Hiram) mkdir /hive/data/genomes/micMur3/bed/cpgIslands cd /hive/data/genomes/micMur3/bed/cpgIslands time (doCpgIslands.pl -dbHost=hgwdev -bigClusterHub=ku \ -workhorse=hgwdev -smallClusterHub=ku micMur3) > do.log 2>&1 & # real 47m4.574s cat fb.micMur3.cpgIslandExt.txt # 52667927 bases of 2386321975 (2.207%) in intersection ############################################################################## # genscan - (DONE - 2017-03-03 - Hiram) mkdir /hive/data/genomes/micMur3/bed/genscan cd /hive/data/genomes/micMur3/bed/genscan time (doGenscan.pl -buildDir=`pwd` -workhorse=hgwdev -dbHost=hgwdev \ -bigClusterHub=ku micMur3) > do.log 2>&1 & # real 64m46.377s # three jobs need window size 2000000, one tiny contig would produce # nothing time (doGenscan.pl -buildDir=`pwd` -workhorse=hgwdev -dbHost=hgwdev \ -continue=makeBed -bigClusterHub=ku micMur3) > makeBed.log 2>&1 & # real 1m26.537s cat fb.micMur3.genscan.txt # 61853048 bases of 2386321975 (2.592%) in intersection cat fb.micMur3.genscanSubopt.txt # 53556163 bases of 2386321975 (2.244%) in intersection ############################################################################# # augustus gene track (DONE - 2017-03-04 - Hiram) mkdir /hive/data/genomes/micMur3/bed/augustus cd /hive/data/genomes/micMur3/bed/augustus time (doAugustus.pl -buildDir=`pwd` -bigClusterHub=ku \ -species=human -dbHost=hgwdev -workhorse=hgwdev micMur3) > do.log 2>&1 & # real 827m10.603s cat fb.micMur3.augustusGene.txt # 54243824 bases of 2386321975 (2.273%) in intersection ############################################################################# # lastz/chain/net swap human/hg38 (DONE - 2017-03-03 - Hiram) # original alignment cd /hive/data/genomes/hg38/bed/lastzMicMur3.2017-03-03 cat fb.hg38.chainMicMur3Link.txt # 906521007 bases of 3049335806 (29.728%) in intersection # and for the swap: mkdir /hive/data/genomes/micMur3/bed/blastz.hg38.swap cd /hive/data/genomes/micMur3/bed/blastz.hg38.swap time (doBlastzChainNet.pl -verbose=2 \ /hive/data/genomes/hg38/bed/lastzMicMur3.2017-03-03/DEF \ -swap -chainMinScore=3000 -chainLinearGap=medium \ -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \ -syntenicNet) > swap.log 2>&1 # real 42m21.629s cat fb.micMur3.chainHg38Link.txt # 880636728 bases of 2386321975 (36.904%) in intersection time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` micMur3 hg38) \ > rbest.log 2>&1 # real 296m23.384s ######################################################################### # lastz/chain/net swap mouse/mm10 (DONE - 2017-03-03 - Hiram) # original alignment cd /hive/data/genomes/mm10/bed/lastzMicMur3.2017-03-03 cat fb.mm10.chainMicMur3Link.txt # 907817373 bases of 2652783500 (34.221%) in intersection time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` mm10 micMur3) \ > rbest.log 2>&1 & # real 522m5.587s # and for the swap: mkdir /hive/data/genomes/micMur3/bed/blastz.mm10.swap cd /hive/data/genomes/micMur3/bed/blastz.mm10.swap time (doBlastzChainNet.pl -verbose=2 \ /hive/data/genomes/mm10/bed/lastzMicMur3.2017-03-03/DEF \ -swap -chainMinScore=3000 -chainLinearGap=medium \ -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \ -syntenicNet) > swap.log 2>&1 # real 71m4.702s cat fb.micMur3.chainMm10Link.txt # 905011854 bases of 2386321975 (37.925%) in intersection time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` micMur3 mm10) \ > rbest.log 2>&1 # real 508m58.716s ############################################################################# # Create kluster run files (DONE - 2017-03-03 - Hiram) # numerator is micMur3 gapless bases "real" as reported by: featureBits -noRandom -noHap micMur3 gap # 89972347 bases of 2349758284 (3.829%) 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 \( 2349758284 / 2861349177 \) \* 1024 # ( 2349758284 / 2861349177 ) * 1024 = 840.915363 # ==> use -repMatch=800 according to size scaled down from 1024 for human. # and rounded down to nearest 50 cd /hive/data/genomes/micMur3 blat micMur3.2bit \ /dev/null /dev/null -tileSize=11 -makeOoc=jkStuff/micMur3.11.ooc \ -repMatch=800 # Wrote 26993 overused 11-mers to jkStuff/micMur3.11.ooc # check non-bridged gaps to see what the typical size is: hgsql -N \ -e 'select * from gap where bridge="no" order by size;' micMur3 \ | sort -k7,7nr | ave -col=7 stdin # there are no non-bridged gaps in this assembly # # all these gap sizes are 100 # # minimum gap size is 100 and produces a reasonable number of lifts # gapToLift -verbose=2 -minGap=10 micMur3 jkStuff/nonBridged.lft \ # -bedFile=jkStuff/nonBridged.bed ######################################################################### # LIFTOVER TO micMur1 (DONE - 2017-03-03 - Hiram) ssh hgwdev mkdir /hive/data/genomes/micMur3/bed/blat.micMur1.2017-03-03 cd /hive/data/genomes/micMur3/bed/blat.micMur1.2017-03-03 time (doSameSpeciesLiftOver.pl -verbose=2 -buildDir=`pwd` \ -ooc=/hive/data/genomes/micMur3/jkStuff/micMur3.11.ooc \ -bigClusterHub=ku -dbHost=hgwdev -workhorse=hgwdev \ micMur3 micMur1) > do.log 2>&1 # real 1569m40.174s # verify the convert link on the test browser is now active from micMur2 to # micMur1 ######################################################################### # LIFTOVER TO micMur2 (DONE - 2017-03-03 - Hiram) ssh hgwdev mkdir /hive/data/genomes/micMur3/bed/blat.micMur2.2017-03-03 cd /hive/data/genomes/micMur3/bed/blat.micMur2.2017-03-03 time (doSameSpeciesLiftOver.pl -verbose=2 -buildDir=`pwd` \ -ooc=/hive/data/genomes/micMur3/jkStuff/micMur3.11.ooc \ -bigClusterHub=ku -dbHost=hgwdev -workhorse=hgwdev \ micMur3 micMur2) > do.log 2>&1 # real 1326m15.222s # verify the convert link on the test browser is now active from micMur2 to # micMur1 ######################################################################## # GENBANK AUTO UPDATE (DONE - 2017-03-05 - Hiram) ssh hgwdev cd $HOME/kent/src/hg/makeDb/genbank git pull # /cluster/data/genbank/data/organism.lst shows: # #organism mrnaCnt estCnt refSeqCnt # Microcebus murinus 99 0 18 # edit etc/genbank.conf to add micMur3 just before macFas5 # micMur3 (Mouse lemur) micMur3.serverGenome = /hive/data/genomes/micMur3/micMur3.2bit micMur3.clusterGenome = /hive/data/genomes/micMur3/micMur3.2bit micMur3.ooc = /hive/data/genomes/micMur3/jkStuff/micMur3.11.ooc micMur3.lift = no micMur3.perChromTables = no micMur3.refseq.mrna.native.pslCDnaFilter = ${finished.refseq.mrna.native.pslCDnaFilter} micMur3.refseq.mrna.xeno.pslCDnaFilter = ${finished.refseq.mrna.xeno.pslCDnaFilter} micMur3.genbank.mrna.native.pslCDnaFilter = ${finished.genbank.mrna.native.pslCDnaFilter} micMur3.genbank.mrna.xeno.pslCDnaFilter = ${finished.genbank.mrna.xeno.pslCDnaFilter} micMur3.genbank.est.native.pslCDnaFilter = ${finished.genbank.est.native.pslCDnaFilter} micMur3.refseq.mrna.native.load = no micMur3.refseq.mrna.xeno.load = yes # DO NOT NEED genbank.mrna.xeno except for human, mouse # the defaults: genbank.mrna.native.load, yes genbank.est.native.load yes # refseq.mrna.native.load yes, refseq.mrna.xeno.load yes # there are no native est micMur3.genbank.est.native.load = no micMur3.downloadDir = micMur3 git commit -m 'adding micMur3 Mouse lemur refs #18984' etc/genbank.conf git push # update /cluster/data/genbank/: make etc-update cd /cluster/data/genbank time ./bin/gbAlignStep -initial micMur3 # logFile: var/build/logs/2017.03.05-06:50:23.micMur3.initalign.log # about 13 hours tail -2 var/build/logs/2017.03.05-06:50:23.micMur3.initalign.log # hgwdev 2017.03.05-19:11:13 micMur3.initalign: Succeeded: micMur3 # hgwdev 2017.03.05-19:11:50 micMur3.initalign: finish # To re-do, rm the dir first: # /cluster/data/genbank/work/initial.micMur3 # load database when finished ssh hgwdev cd /cluster/data/genbank time ./bin/gbDbLoadStep -drop -initialLoad micMur3 # logFile: var/dbload/hgwdev/logs/2017.03.05-19:53:15.micMur3.dbload.log # about 13 minutes tail -1 var/dbload/hgwdev/logs/2017.03.05-19:53:15.micMur3.dbload.log # hgwdev 2017.03.05-20:06:56 micMur3.dbload: finish # enable daily alignment and update of hgwdev cd ~/kent/src/hg/makeDb/genbank git pull # add micMur3 to: # etc/align.dbs etc/hgwdev.dbs git add etc/align.dbs etc/hgwdev.dbs git commit -m 'adding micMur3 to the update alignments refs #18984' etc/align.dbs etc/hgwdev.dbs git push make etc-update ############################################################################# # ncbiRefSeq (TBD - 2016-05-13 - Hiram) mkdir /hive/data/genomes/micMur3/bed/ncbiRefSeq cd /hive/data/genomes/micMur3/bed/ncbiRefSeq # running step wise as this script is still under development time (~/kent/src/hg/utils/automation/doNcbiRefSeq.pl -buildDir=`pwd` \ -bigClusterHub=ku -dbHost=hgwdev \ -stop=download -fileServer=hgwdev -smallClusterHub=ku -workhorse=hgwdev \ refseq vertebrate_other Gallus_gallus \ GCF_000002315.4_Gallus_gallus-5.0 micMur3) > download.log 2>&1 # real 16m29.536s time (~/kent/src/hg/utils/automation/doNcbiRefSeq.pl -buildDir=`pwd` \ -continue=process -bigClusterHub=ku -dbHost=hgwdev \ -stop=process -fileServer=hgwdev -smallClusterHub=ku -workhorse=hgwdev \ refseq vertebrate_other Gallus_gallus \ GCF_000002315.4_Gallus_gallus-5.0 micMur3) > process.log 2>&1 # real 3m58.858s time (~/kent/src/hg/utils/automation/doNcbiRefSeq.pl -buildDir=`pwd` \ -continue=load -bigClusterHub=ku -dbHost=hgwdev \ -stop=load -fileServer=hgwdev -smallClusterHub=ku -workhorse=hgwdev \ refseq vertebrate_other Gallus_gallus \ GCF_000002315.4_Gallus_gallus-5.0 micMur3) > load.log 2>&1 # real 0m33.205s cat fb.ncbiRefSeq.micMur3.txt # 82563006 bases of 1218501075 (6.776%) in intersection featureBits -enrichment micMur3 refGene ncbiRefSeq # refGene 1.181%, ncbiRefSeq 6.776%, both 1.175%, cover 99.49%, # enrich 14.68x ######################################################################### # BLATSERVERS ENTRY (DONE - 2017-03-07 - 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 ("micMur3", "blat1d", "17882", "1", "0"); \ INSERT INTO blatServers (db, host, port, isTrans, canPcr) \ VALUES ("micMur3", "blat1d", "17883", "0", "1");' \ hgcentraltest # test it with some sequence ############################################################################ ## reset default position to same as micMur2 ## (DONE - 2017-03-07 - Hiram) ssh hgwdev hgsql -e 'update dbDb set defaultPos="chr17:30720951-30776185" where name="micMur3";' hgcentraltest ######################################################################### # all.joiner update, downloads and in pushQ - (DONE - 2017-03-06 - Hiram) cd $HOME/kent/src/hg/makeDb/schema # fixup all.joiner until this is a clean output joinerCheck -database=micMur3 -tableCoverage all.joiner joinerCheck -database=micMur3 -times all.joiner joinerCheck -database=micMur3 -keys all.joiner cd /hive/data/genomes/micMur3 time (makeDownloads.pl -workhorse=hgwdev micMur3) > downloads.log 2>&1 # real 22m35.669s # now ready for pushQ entry mkdir /hive/data/genomes/micMur3/pushQ cd /hive/data/genomes/micMur3/pushQ time (makePushQSql.pl micMur3) > micMur3.pushQ.sql 2> stderr.out # real 7m21.629s # check for errors in stderr.out, some are OK, e.g.: # WARNING: hgwdev does not have /gbdb/micMur3/wib/gc5Base.wib # WARNING: hgwdev does not have /gbdb/micMur3/wib/quality.wib # WARNING: hgwdev does not have /gbdb/micMur3/bbi/quality.bw # WARNING: micMur3 does not have seq # WARNING: micMur3 does not have extFile # copy it to hgwbeta scp -p micMur3.pushQ.sql qateam@hgwbeta:/tmp/ ssh qateam@hgwbeta "./bin/x86_64/hgsql qapushq < /tmp/micMur3.pushQ.sql" # in that pushQ entry walk through each entry and see if the # sizes will set properly ######################################################################### # fix common name hgsql -e 'update dbDb set organism="Mouse lemur" where name="micMur3";' \ hgcentraltest hgsql -e 'update dbDb set genome="Mouse lemur" where name="micMur3";' \ hgcentraltest hgsql -e 'delete from genomeClade where genome="Gray mouse lemur";' \ hgcentraltest hgsql -e 'delete from defaultDb where genome="Gray mouse lemur";' \ hgcentraltest #########################################################################