185bb036795666bc9d4d62d962f46eb318f588e0 hiram Fri Aug 30 10:58:44 2019 -0700 completed and in pushQ refs #23771 diff --git src/hg/makeDb/doc/rheMac10/initialBuild.txt src/hg/makeDb/doc/rheMac10/initialBuild.txt index 9e6c0d4..886f3af 100644 --- src/hg/makeDb/doc/rheMac10/initialBuild.txt +++ src/hg/makeDb/doc/rheMac10/initialBuild.txt @@ -1,1002 +1,1030 @@ # for emacs: -*- mode: sh; -*- # This file describes browser build for the rheMac10 # Can use existing photograph (otherwise find one before starting here) ######################################################################### # Initial steps, reuse existing photograph (DONE - 2019-07-01 - Hiram) # To start this initialBuild.txt document, from a previous assembly document: mkdir ~/kent/src/hg/makeDb/doc/rheMac10 cd ~/kent/src/hg/makeDb/doc/rheMac10 sed -e 's/galGal6/rheMac10/g; s/GalGal6/RheMac10/g; s/DONE/TBD/g;' \ ../galGal6/initialBuild.txt > initialBuild.txt mkdir -p /hive/data/genomes/rheMac10/refseq cd /hive/data/genomes/rheMac10 # Can use existing photograph cp -p ../rn6/photoReference.txt ./ cat photoReference.txt photoCreditURL http://www.genome.gov/dmd/img.cfm?node=Photos/Animals/Rat%20(brown%20norway)&id=79111 photoCreditName NHGRI press photos ## download from NCBI cd /hive/data/genomes/rheMac10/refseq time rsync -L -a -P --stats \ rsync://ftp.ncbi.nlm.nih.gov/genomes/refseq/vertebrate_mammalian/Macaca_mulatta/all_assembly_versions/GCF_003339765.1_Mmul_10/ ./ # sent 3,937 bytes received 6,369,691,679 bytes 56,619,516.59 bytes/sec # total size is 6,368,121,788 speedup is 1.00 # real 1m51.641s # this information is from the top of # rheMac10/refseq/*_assembly_report.txt # (aka: rheMac10/refseq/GCF_003339765.1_Mmul_10_assembly_report.txt # Assembly name: Mmul_10 # Organism name: Macaca mulatta (Rhesus monkey) # Taxid: 9544 # BioSample: SAMN09435472 # BioProject: PRJNA476474 # Submitter: The Genome Institute at Washington University School of Medicine # Date: 2019-02-13 # Assembly type: haploid # Release type: major # Assembly level: Chromosome # Genome representation: full # WGS project: QNVO02 # GenBank assembly accession: GCA_003339765.3 # RefSeq assembly accession: GCF_003339765.1 # RefSeq assembly and GenBank assemblies identical: no # ## Assembly-Units: ## GenBank Unit Accession RefSeq Unit Accession Assembly-Unit name ## GCA_003339795.3 GCF_003339795.1 Primary Assembly ## GCF_000005875.1 non-nuclear # # check assembly size for later reference: faSize G*10_genomic.fna.gz # 2971331530 bases (34438805 N's 2936892725 real 1810047126 upper # 1126845599 lower) in 2939 sequences in 1 files # Total size: mean 1011000.9 sd 12006707.4 min 217 (NW_021162293.1) # max 223616942 (NC_041754.1) median 26547 # %37.92 masked total, %38.37 masked real ############################################################################# # establish config.ra file (DONE - Hiram - 2019-07-01) cd /hive/data/genomes/rheMac10 ~/kent/src/hg/utils/automation/prepConfig.pl rheMac10 primate rhesus \ refseq/*_assembly_report.txt > rheMac10.config.ra # compare with previous version to see if it is sane: diff rheMac10.config.ra ../rheMac8/rheMac8.config.ra # verify it really does look sane cat rheMac10.config.ra # config parameters for makeGenomeDb.pl: db rheMac10 clade primate genomeCladePriority 35 scientificName Macaca mulatta commonName rhesus assemblyDate Feb. 2019 assemblyLabel The Genome Institute at Washington University School of Medicine assemblyShortLabel Mmul_10 orderKey 18417 # mitochondrial sequence included in refseq release # mitoAcc NC_005943.1 mitoAcc none fastaFiles /hive/data/genomes/rheMac10/ucsc/*.fa.gz agpFiles /hive/data/genomes/rheMac10/ucsc/*.agp # qualFiles none dbDbSpeciesDir rhesus photoCreditURL http://www.genome.gov/dmd/img.cfm?node=Photos/Animals/Rat%20(brown%20norway)&id=79111 photoCreditName NHGRI press photos ncbiGenomeId 215 ncbiAssemblyId 2345051 ncbiAssemblyName Mmul_10 ncbiBioProject 476474 ncbiBioSample SAMN09435472 genBankAccessionID GCF_003339765.1 taxId 9544 ############################################################################# # setup UCSC named files (DONE - 2019-07-01 - Hiram) mkdir /hive/data/genomes/rheMac10/ucsc cd /hive/data/genomes/rheMac10/ucsc # check for duplicate sequences: time faToTwoBit -noMask ../refseq/G*10_genomic.fna.gz refseq.2bit # real 0m38.595s 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 # remove it later # new option required to ucscCompositeAgp.pl 2016-04-13 time ~/kent/src/hg/utils/automation/ucscCompositeAgp.pl \ ../refseq/G*10_genomic.fna.gz \ ../refseq/*_assembly_structure/Primary_Assembly # constructing refseq.2bit from ../refseq/GCF_000002315.4_Gallus_gallus-5.0_genomic.fna.gz NC_027914.1 chrY NC_041754.1 chr1 NC_041755.1 chr2 NC_041756.1 chr3 NC_041757.1 chr4 NC_041758.1 chr5 NC_041759.1 chr6 NC_041760.1 chr7 NC_041761.1 chr8 NC_041762.1 chr9 NC_041763.1 chr10 NC_041764.1 chr11 NC_041765.1 chr12 NC_041766.1 chr13 NC_041767.1 chr14 NC_041768.1 chr15 NC_041769.1 chr16 NC_041770.1 chr17 NC_041771.1 chr18 NC_041772.1 chr19 NC_041773.1 chr20 NC_041774.1 chrX real 10m33.076s time ~/kent/src/hg/utils/automation/unplacedWithChroms.pl \ ../refseq/*_assembly_structure/Primary_Assembly # processed 340 sequences into chrUn.fa.gz # real 0m30.432s time ~/kent/src/hg/utils/automation/unlocalizedWithChroms.pl \ ../refseq/*_assembly_structure/Primary_Assembly # 11 # 7 # 17 # 2 # 1 # 18 # 16 # 13 # 6 # X # 3 # 9 # 12 # 20 # 14 # 15 # 8 # 4 # 19 # 10 # 5 # processed 291 sequences into chr*_random.gz 21 files real 0m7.023s # bash syntax here mitoAcc=`grep "^# mitoAcc" ../rheMac10.config.ra | awk '{print $NF}'` printf "# mitoAcc %s\n" "$mitoAcc" # mitoAcc NC_005943.1 zcat \ ../refseq/*_assembly_structure/non-nuclear/assem*/AGP/chrMT.comp.agp.gz \ | grep -v "^#" | sed -e "s/^$mitoAcc/chrM/;" > chrM.agp cat chrM.agp # chrM 1 16564 1 O NC_005943.1 1 16564 + printf ">chrM\n" > chrM.fa twoBitToFa -noMask refseq.2bit:$mitoAcc stdout | grep -v "^>" >> chrM.fa gzip chrM.fa faSize chrM.fa.gz # 16564 bases (0 N's 16564 real 16564 upper 0 lower) in 1 sequences in 1 files # verify fasta and AGPs agree time faToTwoBit *.fa.gz test.2bit # real 0m56.726s cat *.agp | checkAgpAndFa stdin test.2bit 2>&1 | tail -4 # All AGP and FASTA entries agree - both files are valid # and no sequence lost from orginal: twoBitToFa test.2bit stdout | faSize stdin # 2971331530 bases (34438805 N's 2936892725 real 2936892725 upper 0 lower) # in 2939 sequences in 1 files # Total size: mean 1011000.9 sd 12006707.4 min 217 (chrUn_NW_021162293v1) # max 223616942 (chr1) median 26547 # same numbers as above (except for upper/lower masking) # 2971331530 bases (34438805 N's 2936892725 real 1810047126 upper # 1126845599 lower) in 2939 sequences in 1 files # Total size: mean 1011000.9 sd 12006707.4 min 217 (NW_021162293.1) # max 223616942 (NC_041754.1) median 26547 # no longer need these temporary 2bit files rm test.2bit refseq.2bit ############################################################################# # Initial database build (DONE - 2019-07-01 - Hiram) # verify sequence and AGP are OK: cd /hive/data/genomes/rheMac10 time (makeGenomeDb.pl -workhorse=hgwdev -dbHost=hgwdev -fileServer=hgwdev \ -stop=agp rheMac10.config.ra) > agp.log 2>&1 # real 2m22.570s # then finish it off: time (makeGenomeDb.pl -workhorse=hgwdev -dbHost=hgwdev \ -fileServer=hgwdev -continue=db rheMac10.config.ra) > db.log 2>&1 # real 15m24.340s # check in the trackDb files created in TemporaryTrackDbCheckout/ # and add rheMac10 to trackDb/makefile # temporary symlink until masked sequence is available cd /hive/data/genomes/rheMac10 ln -s `pwd`/rheMac10.unmasked.2bit /gbdb/rheMac10/rheMac10.2bit ############################################################################## # cpgIslands on UNMASKED sequence (DONE - 2019-07-01 - Hiram) mkdir /hive/data/genomes/rheMac10/bed/cpgIslandsUnmasked cd /hive/data/genomes/rheMac10/bed/cpgIslandsUnmasked time (doCpgIslands.pl -dbHost=hgwdev -bigClusterHub=ku -buildDir=`pwd` \ -tableName=cpgIslandExtUnmasked \ -maskedSeq=/hive/data/genomes/rheMac10/rheMac10.unmasked.2bit \ -workhorse=hgwdev -smallClusterHub=ku rheMac10) > do.log 2>&1 # real 3m25.609s cat fb.rheMac10.cpgIslandExtUnmasked.txt # 38819797 bases of 2936892733 (1.322%) in intersection ############################################################################# # cytoBandIdeo - (DONE - 2019-07-01 - Hiram) mkdir /hive/data/genomes/rheMac10/bed/cytoBand cd /hive/data/genomes/rheMac10/bed/cytoBand makeCytoBandIdeo.csh rheMac10 ############################################################################# # run up idKeys files for chromAlias/ncbiRefSeq (DONE - 2019-07-01 - Hiram) mkdir /hive/data/genomes/rheMac10/bed/idKeys cd /hive/data/genomes/rheMac10/bed/idKeys time (doIdKeys.pl \ -twoBit=/hive/data/genomes/rheMac10/rheMac10.unmasked.2bit \ -buildDir=`pwd` rheMac10) > do.log 2>&1 & # real 4m9.394s cat rheMac10.keySignature.txt # 69c74f5fa18fe2421cabbcd0e80657e9 ############################################################################# # gapOverlap (DONE - 2019-07-01 - Hiram) mkdir /hive/data/genomes/rheMac10/bed/gapOverlap cd /hive/data/genomes/rheMac10/bed/gapOverlap time (doGapOverlap.pl \ -twoBit=/hive/data/genomes/rheMac10/rheMac10.unmasked.2bit rheMac10 ) \ > do.log 2>&1 & # real 1m3.768s # there is only one: wc -l bed.tab # 1 bed.tab cut -f2- bed.tab chr4 51027118 51073686 chr4:51027119-51073686 1000 + 51027118 51073686 0 2 1000,1000 0,45568 cat fb.rheMac10.gapOverlap.txt # 2000 bases of 2971331530 (0.000%) in intersection ############################################################################# # tandemDups (DONE - 2019-07-01 - Hiram) mkdir /hive/data/genomes/rheMac10/bed/tandemDups cd /hive/data/genomes/rheMac10/bed/tandemDups time (~/kent/src/hg/utils/automation/doTandemDup.pl \ -twoBit=/hive/data/genomes/rheMac10/rheMac10.unmasked.2bit rheMac10) \ > do.log 2>&1 & # real 225m10.394s cat fb.rheMac10.tandemDups.txt # 81485851 bases of 2971331530 (2.742%) in intersection bigBedInfo rheMac10.tandemDups.bb | sed -e 's/^/# /;' # version: 4 # fieldCount: 13 # hasHeaderExtension: yes # isCompressed: yes # isSwapped: 0 # extraIndexCount: 0 # itemCount: 1,431,488 # primaryDataSize: 37,737,612 # primaryIndexSize: 176,456 # zoomLevels: 9 # chromCount: 2756 # basesCovered: 1,568,894,232 # meanDepth (of bases covered): 8.122557 # minDepth: 1.000000 # maxDepth: 314.000000 # std of depth: 13.438018 ######################################################################### # ucscToINSDC and ucscToRefSeq table/track (DONE - 2019-07-01 - Hiram) # construct idKeys for the refseq sequence mkdir /hive/data/genomes/rheMac10/refseq/idKeys cd /hive/data/genomes/rheMac10/refseq/idKeys faToTwoBit ../GCF_003339765.1_Mmul_10_genomic.fna.gz rheMac10.refSeq.2bit time (doIdKeys.pl -buildDir=`pwd` \ -twoBit=`pwd`/rheMac10.refSeq.2bit refseqRheMac10) > do.log 2>&1 & # real 4m8.863s cat refseqRheMac10.keySignature.txt # 69c74f5fa18fe2421cabbcd0e80657e9 # and the genbank sequence needs keys too: mkdir /hive/data/genomes/rheMac10/refseq/idKeysGenbank cd /hive/data/genomes/rheMac10/refseq/idKeysGenbank faToTwoBit /hive/data/outside/ncbi/genomes/genbank/vertebrate_mammalian/Macaca_mulatta/all_assembly_versions/GCA_003339765.3_Mmul_10/GCA_003339765.3_Mmul_10_genomic.fna.gz rheMac10.genbank.2bit time (doIdKeys.pl -buildDir=`pwd` \ -twoBit=`pwd`/rheMac10.genbank.2bit genbankRheMac10) > do.log 2>&1 & # real 4m6.755s cat genbankRheMac10.keySignature.txt # 1eb34462822483c9262e98186f71a286 mkdir /hive/data/genomes/rheMac10/bed/chromAlias cd /hive/data/genomes/rheMac10/bed/chromAlias join -t$'\t' ../idKeys/rheMac10.idKeys.txt \ ../../refseq/idKeysGenbank/genbankRheMac10.idKeys.txt | cut -f2- \ | sort -k1,1 | join -t$'\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/rheMac10.idKeys.txt \ ../../refseq/idKeys/refseqRheMac10.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 # should be same line counts throughout: wc -l * ../../chrom.sizes # 2938 ucscToINSDC.bed # 2939 ucscToRefSeq.bed # 2939 ../../chrom.sizes # need to find the accession for the INSDC equivalent to chrM: egrep chrM * # ucscToRefSeq.bed:chrM 0 16564 NC_005943.1 # lookup that accession at NCBI Entrez: AY612638.1 # and add to ucscToINSDC.bed: printf "chrM\t0\t16564\tAY612638.1\n" >> ucscToINSDC.bed # verify: grep chrM * ucscToINSDC.bed:chrM 0 16564 AY612638.1 ucscToRefSeq.bed:chrM 0 16564 NC_005943.1 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 rheMac10 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/" $HOME/kent/src/hg/lib/ucscToINSDC.sql \ | sed -e 's/INSDC/RefSeq/g;' \ | hgLoadSqlTab rheMac10 ucscToRefSeq stdin ucscToRefSeq.bed # should be quiet for all OK checkTableCoords rheMac10 # should cover %100 entirely: featureBits -countGaps rheMac10 ucscToINSDC # 2971331530 bases of 2971331530 (100.000%) in intersection featureBits -countGaps rheMac10 ucscToRefSeq # 2971331530 bases of 2971331530 (100.000%) in intersection ######################################################################### # add chromAlias table (DONE - 2019-07-01 - Hiram) mkdir /hive/data/genomes/rheMac10/bed/chromAlias cd /hive/data/genomes/rheMac10/bed/chromAlias hgsql -N -e 'select chrom,name from ucscToRefSeq;' rheMac10 \ | sort -k1,1 > ucsc.refseq.tab hgsql -N -e 'select chrom,name from ucscToINSDC;' rheMac10 \ | sort -k1,1 > ucsc.genbank.tab ### Adding Ensembl alias with v95 release, after idKeys made: 2019-01-16 join -t$'\t' ../idKeys/rheMac10.idKeys.txt \ ../../ens95/ensRheMac10.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, $3}' \ | sort -k1,1 -k2,2n > ucscToEns.bed cut -f1,4 ucscToEns.bed | sort > ucsc.ensembl.tab wc -l *.bed # 2210 ucscToEns.bed # 2211 ucscToINSDC.bed # 2211 ucscToRefSeq.bed ~/kent/src/hg/utils/automation/chromAlias.pl ucsc.*.tab \ > rheMac10.chromAlias.tab for t in refseq genbank do c0=`cat ucsc.$t.tab | wc -l` c1=`grep $t rheMac10.chromAlias.tab | wc -l` ok="OK" if [ "$c0" -ne "$c1" ]; then ok="ERROR" fi printf "# checking $t: $c0 =? $c1 $ok\n" done # checking refseq: 2939 =? 2939 OK # checking genbank: 2939 =? 2939 OK # verify chrM is here properly: grep chrM rheMac10.chromAlias.tab # AY612638.1 chrM genbank # NC_005943.1 chrM refseq hgLoadSqlTab rheMac10 chromAlias ~/kent/src/hg/lib/chromAlias.sql \ rheMac10.chromAlias.tab ######################################################################### -# fixup search rule for assembly track/gold table (TBD - 2019-07-01 - Hiram) +# fixup search rule for assembly track/gold table (DONE - 2019-07-03 - Hiram) cd ~/kent/src/hg/makeDb/trackDb/rhesus/rheMac10 # preview prefixes and suffixes: hgsql -N -e "select frag from gold;" rheMac10 \ | sed -e 's/[0-9][0-9]*//;' | sort | uniq -c 2 AC.10 2 AC.11 1 AC.13 1 AC.17 4 AC.2 36 AC.3 22 AC.4 8 AC.5 2 AC.6 5 AC.7 4 AC.8 2 AC.9 1 NC_.1 3178 QNVO.1 # implies a rule: '[ANQ][CN][V0-9_][O0-9][0-9]+(\.[0-9]+)?' # verify this rule will find them all and eliminate them all: hgsql -N -e "select frag from gold;" rheMac10 | wc -l # 3268 hgsql -N -e "select frag from gold;" rheMac10 \ | egrep -e '[ANQ][CN][V0-9_][O0-9][0-9]+(\.[0-9]+)?' | wc -l # 3268 hgsql -N -e "select frag from gold;" rheMac10 \ | egrep -v -e '[ANQ][CN][V0-9_][O0-9][0-9]+(\.[0-9]+)?' | wc -l # 0 # hence, add to trackDb/rhesus/rheMac10/trackDb.ra searchTable gold shortCircuit 1 termRegex [ANQ][CN][V0-9_][O0-9][0-9]+(\.[0-9]+)? query select chrom,chromStart,chromEnd,frag from %s where frag like '%s%%' searchPriority 8 -XXX - TBD - # verify searches work in the position box ########################################################################## # running repeat masker (DONE - 2019-07-01 - Hiram) mkdir /hive/data/genomes/rheMac10/bed/repeatMasker cd /hive/data/genomes/rheMac10/bed/repeatMasker time (doRepeatMasker.pl -buildDir=`pwd` \ -bigClusterHub=ku -dbHost=hgwdev -workhorse=hgwdev \ -smallClusterHub=ku rheMac10) > do.log 2>&1 # real 500m43.380s cat faSize.rmsk.txt # 2971331530 bases (34438805 N's 2936892725 real 1399379596 upper # 1537513129 lower) in 2939 sequences in 1 files # Total size: mean 1011000.9 sd 12006707.4 min 217 (chrUn_NW_021162293v1) # max 223616942 (chr1) median 26547 # %51.74 masked total, %52.35 masked real egrep -i "versi|relea" do.log # RepeatMasker version development-$Id: RepeatMasker,v 1.332 2017/04/17 19:01:11 rhubley Exp $ # February 01 2017 (open-4-0-8) 1.332 version of RepeatMasker # CC Dfam_Consensus RELEASE 20181026; * # CC RepBase RELEASE 20181026; time featureBits -countGaps rheMac10 rmsk # 1537510421 bases of 2971331530 (51.745%) in intersection # real 0m40.763s # 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;' rheMac10 \ | bedSingleCover.pl stdin | ave -col=4 stdin | grep "^total" # total 1537510421.000000 # real 0m24.256s ########################################################################## # running simple repeat (DONE - 2019-07-01 - Hiram) # The '-trf409 5' is a bit smaller than human which is 6 mkdir /hive/data/genomes/rheMac10/bed/simpleRepeat cd /hive/data/genomes/rheMac10/bed/simpleRepeat time (doSimpleRepeat.pl -buildDir=`pwd` -bigClusterHub=ku \ -dbHost=hgwdev -workhorse=hgwdev -smallClusterHub=ku \ -trf409=5 rheMac10) > do.log 2>&1 # real 933m29.936s cat fb.simpleRepeat # 158143361 bases of 2936892733 (5.385%) in intersection cd /hive/data/genomes/rheMac10 # using the Window Masker result: cd /hive/data/genomes/rheMac10 # twoBitMask bed/windowMasker/rheMac10.cleanWMSdust.2bit \ # -add bed/simpleRepeat/trfMask.bed rheMac10.2bit # you can safely ignore the warning about fields >= 13 # add to rmsk after it is done: twoBitMask rheMac10.rmsk.2bit \ -add bed/simpleRepeat/trfMask.bed rheMac10.2bit # you can safely ignore the warning about fields >= 13 twoBitToFa rheMac10.2bit stdout | faSize stdin > faSize.rheMac10.2bit.txt cat faSize.rheMac10.2bit.txt # 2971331530 bases (34438805 N's 2936892725 real 1397548789 upper # 1539343936 lower) in 2939 sequences in 1 files # Total size: mean 1011000.9 sd 12006707.4 min 217 (chrUn_NW_021162293v1) # max 223616942 (chr1) median 26547 # %51.81 masked total, %52.41 masked real rm /gbdb/rheMac10/rheMac10.2bit ln -s `pwd`/rheMac10.2bit /gbdb/rheMac10/rheMac10.2bit ######################################################################### # CREATE MICROSAT TRACK (DONE - 2019-07-02 - Hiram) ssh hgwdev mkdir /cluster/data/rheMac10/bed/microsat cd /cluster/data/rheMac10/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 rheMac10 microsat microsat.bed # Read 32040 elements of size 4 from microsat.bed ########################################################################## ## WINDOWMASKER (DONE - 2019-07-01 - Hiram) mkdir /hive/data/genomes/rheMac10/bed/windowMasker cd /hive/data/genomes/rheMac10/bed/windowMasker time (doWindowMasker.pl -buildDir=`pwd` -workhorse=hgwdev \ -dbHost=hgwdev rheMac10) > do.log 2>&1 # real 111m14.660s # Masking statistics cat faSize.rheMac10.cleanWMSdust.txt # 2971331530 bases (34438805 N's 2936892725 real 1792976685 upper # 1143916040 lower) in 2939 sequences in 1 files # Total size: mean 1011000.9 sd 12006707.4 min 217 (chrUn_NW_021162293v1) # max 223616942 (chr1) median 26547 # %38.50 masked total, %38.95 masked real cat fb.rheMac10.rmsk.windowmaskerSdust.txt # 909614480 bases of 2971331530 (30.613%) in intersection ########################################################################## # cpgIslands - (DONE - 2019-07-02 - Hiram) mkdir /hive/data/genomes/rheMac10/bed/cpgIslands cd /hive/data/genomes/rheMac10/bed/cpgIslands time (doCpgIslands.pl -dbHost=hgwdev -bigClusterHub=ku \ -workhorse=hgwdev -smallClusterHub=ku rheMac10) > do.log 2>&1 -XXX - running - Tue Jul 2 07:51:16 PDT 2019 - # real 2m5.105s + # real 3m51.796s cat fb.rheMac10.cpgIslandExt.txt - # 16395346 bases of 1055588482 (1.553%) in intersection + # 21622534 bases of 2936892733 (0.736%) in intersection ############################################################################## # genscan - (DONE - 2019-07-02 - Hiram) mkdir /hive/data/genomes/rheMac10/bed/genscan cd /hive/data/genomes/rheMac10/bed/genscan time (doGenscan.pl -buildDir=`pwd` -workhorse=hgwdev -dbHost=hgwdev \ -bigClusterHub=ku rheMac10) > do.log 2>&1 -XXX - running - Tue Jul 2 07:51:42 PDT 2019 - # real 88m34.900s + # real 134m51.892s cat fb.rheMac10.genscan.txt - # 23911678 bases of 1055588482 (2.265%) in intersection + # 53848328 bases of 2936892733 (1.834%) in intersection cat fb.rheMac10.genscanSubopt.txt - # 24521608 bases of 1055588482 (2.323%) in intersection + # 52550217 bases of 2936892733 (1.789%) in intersection ######################################################################### # Create kluster run files (DONE - 2019-07-01 - Hiram) # numerator is rheMac10 gapless bases "real" as reported by: featureBits -noRandom -noHap rheMac10 gap # 32449617 bases of 2821543288 (1.150%) 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 \( 2821543288 / 2861349177 \) \* 1024 # ( 2821543288 / 2861349177 ) * 1024 = 1009.754542 # ==> use -repMatch=350 according to size scaled down from 1024 for human. # and rounded down to nearest 50 cd /hive/data/genomes/rheMac10 blat rheMac10.2bit \ /dev/null /dev/null -tileSize=11 -makeOoc=jkStuff/rheMac10.11.ooc \ -repMatch=1000 # Wrote 31768 overused 11-mers to jkStuff/rheMac10.11.ooc # rheMac8 at repMatch=900: # Wrote 43065 overused 11-mers to jkStuff/rheMac8.11.ooc # check non-bridged gaps to see what the typical size is: hgsql -N \ -e 'select * from gap where bridge="no" order by size;' rheMac10 \ | sort -k7,7nr | ave -col=7 stdin # min 100.000000 # max 1000000.000000 # minimum gap size is 100 and produces a reasonable number of lifts gapToLift -verbose=2 -minGap=100 rheMac10 jkStuff/rheMac10.nonBridged.lft \ -bedFile=jkStuff/rheMac10.nonBridged.bed wc -l jkStuff/rheMac10.nonBri* # 2979 jkStuff/rheMac10.nonBridged.bed # 2979 jkStuff/rheMac10.nonBridged.lft ######################################################################## -# lastz/chain/net swap human/hg38 (TBD - 2018-10-12 - Hiram) +# lastz/chain/net swap human/hg38 (DONE - 2019-07-03 - Hiram) # original alignment - cd /hive/data/genomes/hg38/bed/lastzRheMac10.2018-10-12 + cd /hive/data/genomes/hg38/bed/lastzRheMac10.2019-07-03 cat fb.hg38.chainRheMac10Link.txt - # 154079940 bases of 3095998939 (4.977%) in intersection + # 2596157811 bases of 3095998939 (83.855%) in intersection cat fb.hg38.chainSynRheMac10Link.txt - # 95877644 bases of 3095998939 (3.097%) in intersection + # 2564291936 bases of 3095998939 (82.826%) in intersection cat fb.hg38.chainRBest.RheMac10.txt - # 106665747 bases of 3095998939 (3.445%) in intersection + # 2422981614 bases of 3095998939 (78.262%) in intersection # and for the swap: mkdir /hive/data/genomes/rheMac10/bed/blastz.hg38.swap cd /hive/data/genomes/rheMac10/bed/blastz.hg38.swap time (doBlastzChainNet.pl -verbose=2 \ - /hive/data/genomes/hg38/bed/lastzRheMac10.2018-10-12/DEF \ - -swap -chainMinScore=5000 -chainLinearGap=loose \ + /hive/data/genomes/hg38/bed/lastzRheMac10.2019-07-03/DEF \ + -swap -chainMinScore=5000 -chainLinearGap=medium \ -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \ -syntenicNet) > swap.log 2>&1 - # real 9m45.514s + # real 61m39.505s cat fb.rheMac10.chainHg38Link.txt - # 120955955 bases of 1055588482 (11.459%) in intersection - + # 2485840115 bases of 2936892733 (84.642%) in intersection cat fb.rheMac10.chainSynHg38Link.txt - # 92597630 bases of 1055588482 (8.772%) in intersection + # 2465210442 bases of 2936892733 (83.939%) in intersection - time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` rheMac10 hg38) > rbest.log 2>&1 & - # real 139m24.408s + time (doRecipBest.pl -workhorse=hgwdev -load -buildDir=`pwd` rheMac10 hg38) > rbest.log 2>&1 + # real 126m29.919s cat fb.rheMac10.chainRBest.Hg38.txt - # 106294585 bases of 1055588482 (10.070%) in intersection + # 2424028492 bases of 2936892733 (82.537%) in intersection ######################################################################### -# lastz/chain/net swap mouse/mm10 (TBD - 2018-10-12 - Hiram) +# lastz/chain/net swap mouse/mm10 (DONE - 2019-07-09 - Hiram) # original alignment - cd /hive/data/genomes/mm10/bed/lastzRheMac10.2018-10-12 + cd /hive/data/genomes/mm10/bed/lastzRheMac10.2019-07-03 + cat fb.mm10.chainRheMac10Link.txt - # 101151132 bases of 2652783500 (3.813%) in intersection + # 923559693 bases of 2652783500 (34.815%) in intersection cat fb.mm10.chainSynRheMac10Link.txt - # 70707720 bases of 2652783500 (2.665%) in intersection + # 878479553 bases of 2652783500 (33.115%) in intersection cat fb.mm10.chainRBest.RheMac10.txt - # 79649474 bases of 2652783500 (3.002%) in intersection + # 879885863 bases of 2652783500 (33.168%) in intersection - # and for the swap: mkdir /hive/data/genomes/rheMac10/bed/blastz.mm10.swap cd /hive/data/genomes/rheMac10/bed/blastz.mm10.swap - time (doBlastzChainNet.pl -verbose=2 \ - /hive/data/genomes/mm10/bed/lastzRheMac10.2018-10-12/DEF \ - -swap -chainMinScore=5000 -chainLinearGap=loose \ + /hive/data/genomes/mm10/bed/lastzRheMac10.2019-07-03/DEF \ + -swap -syntenicNet \ -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \ - -syntenicNet) > swap.log 2>&1 - # real 6m41.043s + -chainMinScore=3000 -chainLinearGap=medium) > swap.log 2>&1 + # real 52m48.045s cat fb.rheMac10.chainMm10Link.txt - # 88539346 bases of 1055588482 (8.388%) in intersection + # 918551088 bases of 2936892733 (31.276%) in intersection + cat fb.rheMac10.chainSynMm10Link.txt + # 876230433 bases of 2936892733 (29.835%) in intersection - time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` rheMac10 mm10) > rbest.log 2>&1 & - # real 94m11.007s + time (doRecipBest.pl -workhorse=hgwdev -load -buildDir=`pwd` rheMac10 mm10) > rbest.log 2>&1 + # real 303m40.303s cat fb.rheMac10.chainRBest.Mm10.txt - # 79474812 bases of 1055588482 (7.529%) in intersection + # 878542993 bases of 2936892733 (29.914%) in intersection + ######################################################################### +# lastz/chain/net swap human/hg19 (DONE - 2019-07-09 - Hiram) + + # original alignment + cd /hive/data/genomes/hg19/bed/lastzRheMac10.2019-07-09 + + cat fb.hg19.chainRheMac10Link.txt + # 2604364199 bases of 2991694177 (87.053%) in intersection + cat fb.hg19.chainSynRheMac10Link.txt + # 2570126144 bases of 2991694177 (85.909%) in intersection + cat fb.hg19.chainRBest.RheMac10.txt + # 2421810991 bases of 2991694177 (80.951%) in intersection + + # and for the swap: + mkdir /hive/data/genomes/rheMac10/bed/blastz.hg19.swap + cd /hive/data/genomes/rheMac10/bed/blastz.hg19.swap + + time (doBlastzChainNet.pl -verbose=2 \ + /hive/data/genomes/hg19/bed/lastzRheMac10.2019-07-09/DEF \ + -swap -chainMinScore=5000 -chainLinearGap=medium \ + -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \ + -syntenicNet) > swap.log 2>&1 + # real 56m29.163s + + cat fb.rheMac10.chainHg19Link.txt + # 2483311773 bases of 2936892733 (84.556%) in intersection + cat fb.rheMac10.chainSynHg19Link.txt + # 2461925388 bases of 2936892733 (83.828%) in intersection + + time (doRecipBest.pl -workhorse=hgwdev -load -buildDir=`pwd` rheMac10 hg19) > rbest.log 2>&1 + # real 112m15.825s + + cat fb.rheMac10.chainRBest.Hg19.txt + # 2423781773 bases of 2936892733 (82.529%) in intersection + +############################################################################## # GENBANK AUTO UPDATE (DONE - 2019-07-03 - Hiram) ssh hgwdev cd $HOME/kent/src/hg/makeDb/genbank git pull # /cluster/data/genbank/data/organism.lst shows: # #organism mrnaCnt estCnt refSeqCnt # Macaca mulatta 381495 60276 5820 # edit etc/genbank.conf to add rheMac10 just before galGal5 # rheMac10 Macaca mulatta (rhesus) (refseq assembly GCF_003339765.1) rheMac10.serverGenome = /hive/data/genomes/rheMac10/rheMac10.2bit rheMac10.ooc = /hive/data/genomes/rheMac10/jkStuff/rheMac10.11.ooc rheMac10.lift = /hive/data/genomes/rheMac10/jkStuff/rheMac10.nonBridged.lft rheMac10.perChromTables = no rheMac10.refseq.mrna.native.pslCDnaFilter = ${finished.refseq.mrna.native.pslCDnaFilter} rheMac10.refseq.mrna.xeno.pslCDnaFilter = ${finished.refseq.mrna.xeno.pslCDnaFilter} rheMac10.genbank.mrna.native.pslCDnaFilter = ${finished.genbank.mrna.native.pslCDnaFilter} rheMac10.genbank.mrna.xeno.pslCDnaFilter = ${finished.genbank.mrna.xeno.pslCDnaFilter} rheMac10.genbank.est.native.pslCDnaFilter = ${finished.genbank.est.native.pslCDnaFilter} rheMac10.genbank.est.xeno.pslCDnaFilter = ${finished.genbank.est.xeno.pslCDnaFilter} rheMac10.downloadDir = rheMac10 # DO NOT NEED genbank.mrna.xeno except for human, mouse(and in this case rhesus) rheMac10.refseq.mrna.native.load = yes rheMac10.refseq.mrna.xeno.load = yes rheMac10.upstreamGeneTbl = refGene # verify the files specified exist before checking in the file: grep ^rheMac10 etc/genbank.conf | grep hive | awk '{print $NF}' | xargs ls -og # -rw-rw-r-- 1 127080 Jul 1 11:03 /hive/data/genomes/rheMac10/jkStuff/rheMac10.11.ooc # -rw-rw-r-- 1 177516 Jul 1 13:16 /hive/data/genomes/rheMac10/jkStuff/rheMac10.nonBridged.lft # -rw-rw-r-- 1 775334369 Jul 2 07:48 /hive/data/genomes/rheMac10/rheMac10.2bit git commit -m "Added rheMac10 rhesus/Macaca mulatta; refs #23771" etc/genbank.conf git push # update /cluster/data/genbank/: make etc-update # enable daily alignment and update of hgwdev cd ~/kent/src/hg/makeDb/genbank git pull # add rheMac10 to: # etc/hgwdev.dbs git add etc/align.dbs etc/hgwdev.dbs git commit -m "Added rheMac10 - rhesus/Macaca mulatta refs #23771" etc/hgwdev.dbs git push make etc-update # wait a few days for genbank magic to take place, the tracks will # appear ############################################################################# # augustus gene track (DONE - 2019-07-02 - Hiram) mkdir /hive/data/genomes/rheMac10/bed/augustus cd /hive/data/genomes/rheMac10/bed/augustus time (doAugustus.pl -buildDir=`pwd` -bigClusterHub=ku \ -species=human -dbHost=hgwdev \ -workhorse=hgwdev rheMac10) > do.log 2>&1 -XXX - running - Tue Jul 2 07:53:20 PDT 2019 - # real 48m48.597s + # real 129m48.296s cat fb.rheMac10.augustusGene.txt - # 25827925 bases of 1055588482 (2.447%) in intersection + # 50002729 bases of 2936892733 (1.703%) in intersection ######################################################################### # ncbiRefSeq (DONE - 2019-07-02 - Hiram) mkdir /hive/data/genomes/rheMac10/bed/ncbiRefSeq cd /hive/data/genomes/rheMac10/bed/ncbiRefSeq # running step wise just to be careful time (~/kent/src/hg/utils/automation/doNcbiRefSeq.pl -buildDir=`pwd` \ -bigClusterHub=ku -dbHost=hgwdev \ -stop=download -fileServer=hgwdev -smallClusterHub=ku -workhorse=hgwdev \ refseq vertebrate_mammalian Macaca_mulatta \ GCF_003339765.1_Mmul_10 rheMac10) > download.log 2>&1 # real 2m3.842s 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_mammalian Macaca_mulatta \ GCF_003339765.1_Mmul_10 rheMac10) > process.log 2>&1 # real 2m6.030s 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_mammalian Macaca_mulatta \ GCF_003339765.1_Mmul_10 rheMac10) > load.log 2>&1 # real 0m27.175s cat fb.ncbiRefSeq.rheMac10.txt # 92462016 bases of 2936892733 (3.148%) in intersection -XXX TBD - # need to add: include ../../refSeqComposite.ra alpha + # add: include ../../refSeqComposite.ra alpha # to the rhesus/rheMac10/trackDb.ra to turn on the track in the browser - # there was one gene that claimed to have a protein, but the - # protein sequence was not included in the protein.faa file - # discovered from joinerCheck - # manual fix to blank out this one protein, to see the entry - hgsql -e 'select * from ncbiRefSeqLink where protAcc="NP_989875.1";' rheMac10 - hgsql -e 'update ncbiRefSeqLink set protAcc="" where protAcc="NP_989875.1";' rheMac10 - # this makes the 'protein' link disappear from the gene details page - # curious that this gene is marked as a non-coding gene anyway ? - # gene: FET1 at chr4:63,102,774-63,105,516- - featureBits -enrichment rheMac10 refGene ncbiRefSeq - # refGene 1.374%, ncbiRefSeq 8.397%, both 1.370%, cover 99.73%, enrich 11.88x + # refGene 0.402%, ncbiRefSeq 3.148%, both 0.402%, cover 99.90%, enrich 31.73x featureBits -enrichment rheMac10 ncbiRefSeq refGene - # ncbiRefSeq 8.397%, refGene 1.374%, both 1.370%, cover 16.32%, enrich 11.88x + # ncbiRefSeq 3.148%, refGene 0.402%, both 0.402%, cover 12.76%, enrich 31.73x featureBits -enrichment rheMac10 ncbiRefSeqCurated refGene - # ncbiRefSeqCurated 1.368%, refGene 1.374%, both 1.364%, cover 99.71%, enrich 72.59x + # ncbiRefSeqCurated 0.401%, refGene 0.402%, both 0.400%, cover 99.66%, enrich 247.79x + featureBits -enrichment rheMac10 refGene ncbiRefSeqCurated - # refGene 1.374%, ncbiRefSeqCurated 1.368%, both 1.364%, cover 99.32%, enrich 72.59x + # refGene 0.402%, ncbiRefSeqCurated 0.401%, both 0.400%, cover 99.33%, enrich 247.79x ######################################################################### # LIFTOVER TO rheMac8 (DONE - 2019-07-02 - Hiram) ssh hgwdev mkdir /hive/data/genomes/rheMac10/bed/blat.rheMac8.2019-07-02 cd /hive/data/genomes/rheMac10/bed/blat.rheMac8.2019-07-02 doSameSpeciesLiftOver.pl -verbose=2 \ -debug -bigClusterHub=ku -dbHost=hgwdev -workhorse=hgwdev \ -ooc=/hive/data/genomes/rheMac10/jkStuff/rheMac10.11.ooc \ rheMac10 rheMac8 time (doSameSpeciesLiftOver.pl -verbose=2 \ -bigClusterHub=ku -dbHost=hgwdev -workhorse=hgwdev \ -ooc=/hive/data/genomes/rheMac10/jkStuff/rheMac10.11.ooc \ rheMac10 rheMac8) > doLiftOverToRheMac8.log 2>&1 -XXX - running - Tue Jul 2 08:11:05 PDT 2019 - # real 156m30.215s + # real 268m29.927s - # see if the liftOver menus function in the browser from rheMac10 to galGal5 + # see if the liftOver menus function in the browser from rheMac10 to rheMac8 ######################################################################### -# BLATSERVERS ENTRY (TBD - 2018-10-12 - Hiram) +# BLATSERVERS ENTRY (DONE - 2019-07-09 - 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 ("rheMac10", "blat1a", "17892", "1", "0"); \ + VALUES ("rheMac10", "blat1a", "17898", "1", "0"); \ INSERT INTO blatServers (db, host, port, isTrans, canPcr) \ - VALUES ("rheMac10", "blat1a", "17893", "0", "1");' \ + VALUES ("rheMac10", "blat1a", "17899", "0", "1");' \ hgcentraltest # test it with some sequence ############################################################################ -## reset default position to MEPE gene (egg shell protein) -## (TBD - 2018-10-12 - Hiram) +## reset default position to same as rheMac8 +## (DONE - 2019-07-09 - Hiram) # as found from the galGal5 to rheMac10 liftOver ssh hgwdev - hgsql -e 'update dbDb set defaultPos="chr4:45667017-45672928" + hgsql -e 'update dbDb set defaultPos="chr3:70672926-70708108" where name="rheMac10";' hgcentraltest ######################################################################### # crispr 10K shoulders (TBD - 2018-10-16 - Hiram) # working on this script, adding the indexFa step: time (~/kent/src/hg/utils/automation/doCrispr.pl \ -stop=indexFa -buildDir=`pwd` -smallClusterHub=ku rheMac10 ncbiRefSeq) \ > indexFa.log 2>&1 # real 23m26.694s time (~/kent/src/hg/utils/automation/doCrispr.pl \ -continue=ranges -stop=guides -buildDir=`pwd` -smallClusterHub=ku \ rheMac10 ncbiRefSeq) > guides.log 2>&1 # real 2m50.758s # adding the /dev/shm/ setup rsync for the indexed Fa # performed manually to work out the procedure time (~/kent/src/hg/utils/automation/doCrispr.pl \ -continue=specScores -stop=specScores -buildDir=`pwd` \ -smallClusterHub=ku rheMac10 ncbiRefSeq) > specScores.log # had about half of ku for about half this time: # Completed: 884922 of 884922 jobs # CPU time in finished jobs: 35872791s 597879.85m 9964.66h 415.19d 1.138 y # IO & Wait Time: 899261s 14987.69m 249.79h 10.41d 0.029 y # Average job time: 42s 0.69m 0.01h 0.00d # Longest finished job: 88s 1.47m 0.02h 0.00d # Submission to last job: 48045s 800.75m 13.35h 0.56d time find tmp/outGuides -type f | xargs cut -f3-6 > ../specScores.tab # real 236m17.220s wc -l specScores.tab # 66451712 specScores.tab time (~/kent/src/hg/utils/automation/doCrispr.pl \ -continue=effScores -stop=load \ -buildDir=`pwd` -smallClusterHub=ku rheMac10 ncbiRefSeq) \ > load.log # real 307m41.143s ######################################################################### -# all.joiner update, downloads and in pushQ - (TBD - 2018-10-17 - Hiram) +# all.joiner update, downloads and in pushQ - (DONE - 2019-07-03,08-30 - Hiram) xyz cd $HOME/kent/src/hg/makeDb/schema # verify all the business is done for release ~/kent/src/hg/utils/automation/verifyBrowser.pl rheMac10 # fixup all.joiner until this is a clean output joinerCheck -database=rheMac10 -tableCoverage all.joiner joinerCheck -database=rheMac10 -times all.joiner joinerCheck -database=rheMac10 -keys all.joiner # when clean, check in: - git commit -m 'adding rules for rheMac10 refs #22113' all.joiner + git commit -m 'adding rules for rheMac10 and regenRn0 refs #23771 #21578' all.joiner git push # run up a 'make alpha' in hg/hgTables to get this all.joiner file # into the hgwdev/genome-test system cd /hive/data/genomes/rheMac10 time (makeDownloads.pl rheMac10) > downloads.log 2>&1 - # real 10m7.605s + # real 17m47.024s # now ready for pushQ entry mkdir /hive/data/genomes/rheMac10/pushQ cd /hive/data/genomes/rheMac10/pushQ - time (makePushQSql.pl -redmineList rheMac10) > rheMac10.pushQ.sql 2> stderr.out - # real 9m58.779s - - # remove the extra chainNet files from the listings: - sed -i -e "/etNig1/d" redmine.rheMac10.file.list - sed -i -e "/asAcu1/d" redmine.rheMac10.file.list - sed -i -e "/etNig1/d" redmine.rheMac10.table.list - sed -i -e "/onAlb1/d" redmine.rheMac10.table.list - sed -i -e "/asAcu1/d" redmine.rheMac10.table.list - sed -i -e "/Stickleback/d" redmine.rheMac10.releaseLog.txt - sed -i -e "/Tetraodon/d" redmine.rheMac10.releaseLog.txt - sed -i -e "/sparrow/d" redmine.rheMac10.releaseLog.txt + time ($HOME/kent/src/hg/utils/automation/makePushQSql.pl -redmineList rheMac10) > rheMac10.pushQ.sql 2> stderr.out + # real 15m52.548s + # remove the tandemDups and gapOverlap from the file list: sed -i -e "/tandemDups/d" redmine.rheMac10.table.list sed -i -e "/Tandem Dups/d" redmine.rheMac10.releaseLog.txt sed -i -e "/gapOverlap/d" redmine.rheMac10.table.list sed -i -e "/Gap Overlaps/d" redmine.rheMac10.releaseLog.txt - # real 7m21.629s # check for errors in stderr.out, some are OK, e.g.: # WARNING: hgwdev does not have /gbdb/rheMac10/wib/gc5Base.wib # WARNING: hgwdev does not have /gbdb/rheMac10/wib/quality.wib # WARNING: hgwdev does not have /gbdb/rheMac10/bbi/quality.bw # WARNING: rheMac10 does not have seq # WARNING: rheMac10 does not have extFile + + # verify the file list does correctly match to files + cat redmine.rheMac10.file.list | while read L +do + eval ls $L > /dev/null +done + # should be silent, missing files will show as errors + + # verify database tables, how many to expect: + wc -l redmine.rheMac10.table.list + # 63 redmine.rheMac10.table.list + + # how many actual: + awk -F'.' '{printf "hgsql -N %s -e '"'"'show table status like \"%s\";'"'"'\n", $1, $2}' redmine.rheMac10.table.list | sh | wc -l + # 63 + + # would be a smaller number actual if some were missing + # add the path names to the listing files in the redmine issue # in the three appropriate entry boxes: # /hive/data/genomes/rheMac10/pushQ/redmine.rheMac10.file.list # /hive/data/genomes/rheMac10/pushQ/redmine.rheMac10.releaseLog.txt # /hive/data/genomes/rheMac10/pushQ/redmine.rheMac10.table.list #########################################################################