c5dc7044d76420830c68a063b195599f655e8e5d hiram Fri Jun 12 12:03:39 2020 -0700 running repeat masker refs #25720 diff --git src/hg/makeDb/doc/panPan3/initialBuild.txt src/hg/makeDb/doc/panPan3/initialBuild.txt index 1feb8de..f883b86 100644 --- src/hg/makeDb/doc/panPan3/initialBuild.txt +++ src/hg/makeDb/doc/panPan3/initialBuild.txt @@ -1,1054 +1,1064 @@ # for emacs: -*- mode: sh; -*- # This file describes browser build for the panPan3 # Can use existing photograph (otherwise find one before starting here) ######################################################################### # Initial steps, reuse existing photograph (DONE - 2020-06-12 - Hiram) # Might be a different individual, requests made # To start this initialBuild.txt document, from a previous assembly document: mkdir ~/kent/src/hg/makeDb/doc/panPan3 cd ~/kent/src/hg/makeDb/doc/panPan3 sed -e 's/gorGor6/panPan3/g; s/GorGor6/PanPan3/g; s/DONE/TBD/g;' \ ../gorGor6/initialBuild.txt > initialBuild.txt mkdir -p /hive/data/genomes/panPan3/refseq cd /hive/data/genomes/panPan3 # Can use existing photograph cp -p ../panPan2/photoReference.txt ./ cat photoReference.txt photoCreditURL http://a-z-animals.com/animals/bonobo/pictures/2955/ photoCreditName Photo courtesy of Kabir Bakie ## download from NCBI cd /hive/data/genomes/panPan3/refseq time rsync -L -a -P --stats \ rsync://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/013/052/645/GCF_013052645.1_Mhudiblu_PPA_v0/ ./ # sent 3,203 bytes received 6,058,365,683 bytes 56,886,092.83 bytes/sec # total size is 6,056,874,807 speedup is 1.00 # real 1m45.870s # this information is from the top of # panPan3/refseq/*_assembly_report.txt # (aka: panPan3/refseq/GCF_013052645.1_Mhudiblu_PPA_v0_assembly_report.txt ) # Assembly name: Mhudiblu_PPA_v0 # Organism name: Pan paniscus (pygmy chimpanzee) # Isolate: Mhudiblu (Carbone #601152) # Sex: female # Taxid: 9597 # BioSample: SAMN11123633 # BioProject: PRJNA526933 # Submitter: University of Washington # Date: 2020-05-15 # Assembly type: haploid # Release type: major # Assembly level: Chromosome # Genome representation: full # WGS project: SSBP01 # Assembly method: FALCON v. (git hash: 91e700c4) Nov 2015 # Expected final version: no # Genome coverage: 85.0x # Sequencing technology: PacBio RSII; Illumina # GenBank assembly accession: GCA_013052645.1 # RefSeq assembly accession: GCF_013052645.1 # RefSeq assembly and GenBank assemblies identical: no # ## Assembly-Units: ## GenBank Unit Accession RefSeq Unit Accession Assembly-Unit name ## GCA_013052655.1 GCF_013052655.1 Primary Assembly ## GCF_000029195.1 non-nuclear # check assembly size for later reference: faSize G*0_genomic.fna.gz # 3051901337 bases (36551040 N's 3015350297 real 1802830734 upper # 1212519563 lower) in 4293 sequences in 1 files # Total size: mean 710901.8 sd 9447605.7 min 209 (NW_023258064.1) # max 224621958 (NC_048239.1) median 32647 # %39.73 masked total, %40.21 masked real ############################################################################# # establish config.ra file (DONE - Hiram - 2020-06-12) cd /hive/data/genomes/panPan3 ~/kent/src/hg/utils/automation/prepConfig.pl panPan3 mammal bonobo \ refseq/*_assembly_report.txt > panPan3.config.ra # verify it is sane: diff panPan3.config.ra ../panPan2/panPan2.config.ra # fixup commonName, from: commonName Pygmy chimpanzee to commonName Bonobo genomeCladePriority 35 to genomeCladePriority 15 orderKey 17442 to orderKey 2623 # verify it really does look sane cat panPan3.config.ra # config parameters for makeGenomeDb.pl: db panPan3 clade mammal genomeCladePriority 15 scientificName Pan paniscus commonName Bonobo assemblyDate May 2020 assemblyLabel University of Washington assemblyShortLabel Mhudiblu_PPA_v0 orderKey 2623 # mitochondrial sequence included in refseq release # mitoAcc NC_001644.1 mitoAcc none fastaFiles /hive/data/genomes/panPan3/ucsc/*.fa.gz agpFiles /hive/data/genomes/panPan3/ucsc/*.agp # qualFiles none dbDbSpeciesDir bonobo photoCreditURL http://a-z-animals.com/animals/bonobo/pictures/2955/ photoCreditName Photo courtesy of Kabir Bakie ncbiGenomeId 10729 ncbiAssemblyId 7133581 ncbiAssemblyName Mhudiblu_PPA_v0 ncbiBioProject 526933 ncbiBioSample SAMN11123633 genBankAccessionID GCF_013052645.1 taxId 9597 ############################################################################# # setup UCSC named files (DONE - 2020-06-12 - Hiram) mkdir /hive/data/genomes/panPan3/ucsc cd /hive/data/genomes/panPan3/ucsc # check for duplicate sequences: time faToTwoBit -noMask ../refseq/G*0_genomic.fna.gz refseq.2bit # real 0m44.404s 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 time ~/kent/src/hg/utils/automation/ucscCompositeAgp.pl \ ../refseq/G*0_genomic.fna.gz \ ../refseq/*_assembly_structure/Primary_Assembly NC_048239.1 chr1 NC_048240.1 chr2A NC_048241.1 chr2B NC_048242.1 chr3 NC_048243.1 chr4 NC_048244.1 chr5 NC_048245.1 chr6 NC_048246.1 chr7 NC_048247.1 chr8 NC_048248.1 chr9 NC_048249.1 chr10 NC_048250.1 chr11 NC_048251.1 chr12 NC_048252.1 chr13 NC_048253.1 chr14 NC_048254.1 chr15 NC_048255.1 chr16 NC_048256.1 chr17 NC_048257.1 chr18 NC_048258.1 chr19 NC_048259.1 chr20 NC_048260.1 chr21 NC_048261.1 chr22 NC_048262.1 chrX # real 11m31.473s time ~/kent/src/hg/utils/automation/unplacedWithChroms.pl \ ../refseq/*_assembly_structure/Primary_Assembly # processed 4268 sequences into chrUn.fa.gz # real 0m50.843s # there are *no* unlocalized sequences time ~/kent/src/hg/utils/automation/unlocalizedWithChroms.pl \ ../refseq/*_assembly_structure/Primary_Assembly # bash syntax here mitoAcc=`grep "^# mitoAcc" ../panPan3.config.ra | awk '{print $NF}'` printf "# mitoAcc %s\n" "$mitoAcc" # mitoAcc NC_001644.1 zcat \ ../refseq/*_assembly_structure/non-nuclear/assem*/AGP/chrMT.comp.agp.gz \ | grep -v "^#" | sed -e "s/^$mitoAcc/chrM/;" > chrM.agp cat chrM.agp # chrM 1 16563 1 O NC_001644.1 1 16563 + printf ">chrM\n" > chrM.fa twoBitToFa -noMask refseq.2bit:$mitoAcc stdout | grep -v "^>" >> chrM.fa gzip chrM.fa faSize chrM.fa.gz # 16563 bases (0 N's 16563 real 16563 upper 0 lower) in 1 sequences in 1 files # verify fasta and AGPs agree time faToTwoBit *.fa.gz test.2bit # real 0m55.327s 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 # 3051901337 bases (36551040 N's 3015350297 real 3015350297 upper # 0 lower) in 4293 sequences in 1 files # same numbers as above (except for upper/lower masking) # 3051901337 bases (36551040 N's 3015350297 real 1802830734 upper # 1212519563 lower) in 4293 sequences in 1 files # no longer need these temporary 2bit files rm test.2bit refseq.2bit ############################################################################# # Initial database build (DONE - 2020-06-12 - Hiram) # verify sequence and AGP are OK: cd /hive/data/genomes/panPan3 time (makeGenomeDb.pl -workhorse=hgwdev -dbHost=hgwdev -fileServer=hgwdev \ -stop=agp panPan3.config.ra) > agp.log 2>&1 # real 2m32.140s # then finish it off: time (makeGenomeDb.pl -workhorse=hgwdev -dbHost=hgwdev \ -fileServer=hgwdev -continue=db panPan3.config.ra) > db.log 2>&1 -XXX - running - Fri Jun 12 10:29:45 PDT 2020 - # real 17m28.042s + # real 16m31.749s + + # fixing trackDb step: (new files required in trackDb source fetch) + time (~/kent/src/hg/utils/automation/makeGenomeDb.pl -workhorse=hgwdev \ + -dbHost=hgwdev -continue=trackDb -fileServer=hgwdev \ + panPan3.config.ra) > trackDb.log 2>&1 + # real 0m6.470s # check in the trackDb files created in TemporaryTrackDbCheckout/ # and add panPan3 to trackDb/makefile # temporary symlink until masked sequence is available cd /hive/data/genomes/panPan3 ln -s `pwd`/panPan3.unmasked.2bit /gbdb/panPan3/panPan3.2bit ############################################################################# -# check gap table vs NCBI gap file (TBD - 2019-11-19 - Hiram) +# check gap table vs NCBI gap file (DONE - 2020-06-12 - Hiram) mkdir /hive/data/genomes/panPan3/bed/gap cd /hive/data/genomes/panPan3/bed/gap zgrep -v "^#" ../../refseq/G*_gaps.txt.gz \ | awk '{printf "%s\t%d\t%d\t%s_%s\n", $1,$2-1,$3,$5,$6}' \ | sort -k1,1 -k2,2n > refseq.gap.bed # type survey: cut -f4 *.bed | sort | uniq -c - # 220 between_scaffolds_na - # 639 within_scaffold_map + # 64 between_scaffolds_na + # 619 within_scaffold_map # how much defined by NCBI: awk '{print $3-$2}' *.bed | ave stdin | grep -w total - # total 45844299.000000 + # total 36551040.000000 # how much in the gap table: hgsql -e 'select * from gap;' panPan3 | awk '{print $4-$3}' \ | ave stdin | grep -w total - # total 45844299.000000 + # total 36551040.000000 # equal amounts, no need to adjust the gap table ############################################################################## -# cpgIslands on UNMASKED sequence (TBD - 2019-11-19 - Hiram) +# cpgIslands on UNMASKED sequence (DONE - 2020-06-12 - Hiram) mkdir /hive/data/genomes/panPan3/bed/cpgIslandsUnmasked cd /hive/data/genomes/panPan3/bed/cpgIslandsUnmasked time (doCpgIslands.pl -dbHost=hgwdev -bigClusterHub=ku -buildDir=`pwd` \ -tableName=cpgIslandExtUnmasked \ -maskedSeq=/hive/data/genomes/panPan3/panPan3.unmasked.2bit \ -workhorse=hgwdev -smallClusterHub=ku panPan3) > do.log 2>&1 - # real 4m13.285s + # real 4m48.939s cat fb.panPan3.cpgIslandExtUnmasked.txt - # 28001209 bases of 2999027915 (0.934%) in intersection + # 29049864 bases of 3015350297 (0.963%) in intersection ############################################################################# -# cytoBandIdeo - (TBD - 2019-11-19 - Hiram) +# cytoBandIdeo - (DONE - 2020-06-12 - Hiram) mkdir /hive/data/genomes/panPan3/bed/cytoBand cd /hive/data/genomes/panPan3/bed/cytoBand makeCytoBandIdeo.csh panPan3 ############################################################################# -# run up idKeys files for chromAlias/ncbiRefSeq (TBD - 2019-11-19 - Hiram) +# run up idKeys files for chromAlias/ncbiRefSeq (DONE - 2020-06-12 - Hiram) mkdir /hive/data/genomes/panPan3/bed/idKeys cd /hive/data/genomes/panPan3/bed/idKeys time (doIdKeys.pl \ -twoBit=/hive/data/genomes/panPan3/panPan3.unmasked.2bit \ -buildDir=`pwd` panPan3) > do.log 2>&1 & - # real 2m48.092s + # real 22m22.873s cat panPan3.keySignature.txt - # 10c42ee6ea4a90775c5da9d8b83854aa + # 25a9ac3ecf4f0b51c5a213bd22ddd73f ############################################################################# -# gapOverlap (TBD - 2019-11-19 - Hiram) +# gapOverlap (DONE - 2020-06-12 - Hiram) mkdir /hive/data/genomes/panPan3/bed/gapOverlap cd /hive/data/genomes/panPan3/bed/gapOverlap time (doGapOverlap.pl \ -twoBit=/hive/data/genomes/panPan3/panPan3.unmasked.2bit panPan3 ) \ > do.log 2>&1 & - # real 1m50.075s + # real 1m49.512s # there is only one: wc -l bed.tab # 1 bed.tab cut -f2- bed.tab -chrX 66519024 66677016 chrX:66519025-66677016 1000 + 66519024 66677016 0 2 1000,1000 0,156992 +#chr7 144505525 144507630 chr7:144505526-144507630 803 + +# 144505525 144507630 0 2 803,803 0,1302 cat fb.panPan3.gapOverlap.txt - # 2000 bases of 3044872214 (0.000%) in intersection + # 1606 bases of 3051901337 (0.000%) in intersection ############################################################################# -# tandemDups (TBD - 2019-11-19 - Hiram) +# tandemDups (DONE - 2020-06-12 - Hiram) mkdir /hive/data/genomes/panPan3/bed/tandemDups cd /hive/data/genomes/panPan3/bed/tandemDups time (~/kent/src/hg/utils/automation/doTandemDup.pl \ -twoBit=/hive/data/genomes/panPan3/panPan3.unmasked.2bit panPan3) \ > do.log 2>&1 & +XXX - running - Fri Jun 12 11:33:27 PDT 2020 # real 188m34.598s cat fb.panPan3.tandemDups.txt # 155315479 bases of 3044872214 (5.101%) in intersection bigBedInfo panPan3.tandemDups.bb | sed -e 's/^/# /;' # version: 4 # fieldCount: 13 # hasHeaderExtension: yes # isCompressed: yes # isSwapped: 0 # extraIndexCount: 0 # itemCount: 2,822,307 # primaryDataSize: 72,710,994 # primaryIndexSize: 292,560 # zoomLevels: 9 # chromCount: 5335 # basesCovered: 1,635,503,835 # meanDepth (of bases covered): 14.396921 # minDepth: 1.000000 # maxDepth: 381.000000 # std of depth: 29.341113 ######################################################################### -# ucscToINSDC and ucscToRefSeq table/track (TBD - 2019-11-19 - Hiram) +# ucscToINSDC and ucscToRefSeq table/track (DONE - 2020-06-12 - Hiram) # construct idKeys for the refseq sequence mkdir /hive/data/genomes/panPan3/refseq/idKeys cd /hive/data/genomes/panPan3/refseq/idKeys faToTwoBit ../GCF_*0_genomic.fna.gz panPan3.refSeq.2bit time (doIdKeys.pl -buildDir=`pwd` \ -twoBit=`pwd`/panPan3.refSeq.2bit refseqPanPan3) > do.log 2>&1 & - # real 2m50.723s + # real 6m11.312s cat refseqPanPan3.keySignature.txt - # 10c42ee6ea4a90775c5da9d8b83854aa + # 25a9ac3ecf4f0b51c5a213bd22ddd73f # and the genbank sequence needs keys too: mkdir /hive/data/genomes/panPan3/refseq/idKeysGenbank cd /hive/data/genomes/panPan3/refseq/idKeysGenbank - faToTwoBit /hive/data/outside/ncbi/genomes/genbank/vertebrate_mammalian/Gorilla_gorilla/all_assembly_versions/GCA_008122165.1_Kamilah_GGO_v0/GCA_008122165.1_Kamilah_GGO_v0_genomic.fna.gz panPan3.genbank.2bit + faToTwoBit /hive/data/outside/ncbi/genomes/GCA/013/052/645/GCA_013052645.1_Mhudiblu_PPA_v0/GCA_013052645.1_Mhudiblu_PPA_v0_genomic.fna.gz panPan3.genbank.2bit time (doIdKeys.pl -buildDir=`pwd` \ -twoBit=`pwd`/panPan3.genbank.2bit genbankPanPan3) > do.log 2>&1 & +XXX - running - Fri Jun 12 12:03:06 PDT 2020 # real 3m11.098s cat genbankPanPan3.keySignature.txt # 84734b343949ddf1e28b453d25d3ddf7 mkdir /hive/data/genomes/panPan3/bed/chromAlias cd /hive/data/genomes/panPan3/bed/chromAlias join -t$'\t' ../idKeys/panPan3.idKeys.txt \ ../../refseq/idKeysGenbank/genbankPanPan3.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/panPan3.idKeys.txt \ ../../refseq/idKeys/refseqPanPan3.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 # 5485 ucscToINSDC.bed # 5486 ucscToRefSeq.bed # 5486 ../../chrom.sizes # need to find the accession for the INSDC equivalent to chrM: egrep chrM * # ucscToRefSeq.bed:chrM 0 16412 NC_011120.1 # lookup that accession at NCBI Entrez: X93347.1 # and add to ucscToINSDC.bed: printf "chrM\t0\t16564\tAY612638.1\n" >> ucscToINSDC.bed # verify: grep chrM * ucscToINSDC.bed:chrM 0 16412 X93347.1 ucscToRefSeq.bed:chrM 0 16412 NC_011120.1 export chrSize=`cut -f1 ucscToINSDC.bed | awk '{print length($0)}' | sort -n | tail -1` echo $chrSize # 26 # use the $chrSize in this sed sed -e "s/21/$chrSize/" $HOME/kent/src/hg/lib/ucscToINSDC.sql \ | hgLoadSqlTab panPan3 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 $chrSize # 26 sed -e "s/21/$chrSize/" $HOME/kent/src/hg/lib/ucscToINSDC.sql \ | sed -e 's/INSDC/RefSeq/g;' \ | hgLoadSqlTab panPan3 ucscToRefSeq stdin ucscToRefSeq.bed # should be quiet for all OK checkTableCoords panPan3 # should cover %100 entirely: featureBits -countGaps panPan3 ucscToINSDC # 3044872214 bases of 3044872214 (100.000%) in intersection featureBits -countGaps panPan3 ucscToRefSeq # 3044872214 bases of 3044872214 (100.000%) in intersection ######################################################################### # add chromAlias table (TBD - 2019-11-19 - Hiram) mkdir /hive/data/genomes/panPan3/bed/chromAlias cd /hive/data/genomes/panPan3/bed/chromAlias hgsql -N -e 'select chrom,name from ucscToRefSeq;' panPan3 \ | sort -k1,1 > ucsc.refseq.tab hgsql -N -e 'select chrom,name from ucscToINSDC;' panPan3 \ | sort -k1,1 > ucsc.genbank.tab wc -l *.tab # 5486 ucsc.genbank.tab # 5486 ucsc.refseq.tab ~/kent/src/hg/utils/automation/chromAlias.pl ucsc.*.tab \ > panPan3.chromAlias.tab for t in refseq genbank do c0=`cat ucsc.$t.tab | wc -l` c1=`grep $t panPan3.chromAlias.tab | wc -l` ok="OK" if [ "$c0" -ne "$c1" ]; then ok="ERROR" fi printf "# checking $t: $c0 =? $c1 $ok\n" done # checking refseq: 5486 =? 5486 OK # checking genbank: 5486 =? 5486 OK # verify chrM is here properly: grep chrM panPan3.chromAlias.tab # NC_011120.1 chrM refseq # X93347.1 chrM genbank hgLoadSqlTab panPan3 chromAlias ~/kent/src/hg/lib/chromAlias.sql \ panPan3.chromAlias.tab ######################################################################### -# fixup search rule for assembly track/gold table (TBD - 2019-11-19 - Hiram) - cd ~/kent/src/hg/makeDb/trackDb/gorilla/panPan3 +# fixup search rule for assembly track/gold table (DONE - 2020-06-12 - Hiram) + cd ~/kent/src/hg/makeDb/trackDb/bonobo/panPan3 # preview prefixes and suffixes: hgsql -N -e "select frag from gold;" panPan3 \ - | sed -e 's/[0-9][0-9]*//;' | sort | uniq -c - 1 NC_.1 - 6344 SRLZ.1 + | sed -e 's/[0-9][0-9]*//;' | sort | uniq -c | sed -e 's/^/# /;' +# 1 NC_.1 +# 4975 SSBP.1 - # implies a rule: '[NS][CR][L0-9_][Z0-9][0-9]+(\.[0-9]+)?' + # implies a rule: '[NS][CS][B0-9_][P0-9][0-9]+(\.[0-9]+)?' # verify this rule will find them all and eliminate them all: hgsql -N -e "select frag from gold;" panPan3 | wc -l - # 6345 + # 4976 hgsql -N -e "select frag from gold;" panPan3 \ - | egrep -e '[NS][CR][L0-9_][Z0-9][0-9]+(\.[0-9]+)?' | wc -l - # 6345 + | egrep -e '[NS][CS][B0-9_][P0-9][0-9]+(\.[0-9]+)?' | wc -l + # 4976 hgsql -N -e "select frag from gold;" panPan3 \ - | egrep -v -e '[NS][CR][L0-9_][Z0-9][0-9]+(\.[0-9]+)?' | wc -l + | egrep -v -e '[NS][CS][B0-9_][P0-9][0-9]+(\.[0-9]+)?' | wc -l # 0 # hence, add to trackDb/rhesus/panPan3/trackDb.ra searchTable gold shortCircuit 1 -termRegex [NS][CR][L0-9_][Z0-9][0-9]+(\.[0-9]+)? +termRegex [NS][CS][B0-9_][P0-9][0-9]+(\.[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 (TBD - 2019-11-19 - Hiram) +# running repeat masker (DONE - 2020-06-12 - Hiram) mkdir /hive/data/genomes/panPan3/bed/repeatMasker cd /hive/data/genomes/panPan3/bed/repeatMasker time (doRepeatMasker.pl -buildDir=`pwd` \ -bigClusterHub=ku -dbHost=hgwdev -workhorse=hgwdev \ -smallClusterHub=ku panPan3) > do.log 2>&1 +XXX - running - Fri Jun 12 11:39:31 PDT 2020 # real 415m10.888s cat faSize.rmsk.txt # 3044872214 bases (45844299 N's 2999027915 real 1492721019 upper # 1506306896 lower) in 5486 sequences in 1 files # Total size: mean 555025.9 sd 8254410.8 min 202 (chrUn_NW_022154607v1) # max 219763114 (chr1) median 29244 # %49.47 masked total, %50.23 masked real egrep -i "versi|relea" do.log # RepeatMasker version development-$Id: RepeatMasker,v 1.332 2017/04/17 19:01:11 rhubley Exp $ # grep version of RepeatMasker$ /hive/data/staging/data/RepeatMasker/RepeatMasker # February 01 2017 (open-4-0-8) 1.332 version of RepeatMasker # grep RELEASE /hive/data/staging/data/RepeatMasker/Libraries/RepeatMaskerLib.embl # CC Dfam_Consensus RELEASE 20181026; * # CC RepBase RELEASE 20181026; * time featureBits -countGaps panPan3 rmsk # 1506305481 bases of 3044872214 (49.470%) in intersection # real 0m41.857s # 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;' panPan3 \ | bedSingleCover.pl stdin | ave -col=4 stdin | grep "^total" # total 1506305481.000000 # real 0m22.271s ########################################################################## -# running simple repeat (TBD - 2019-11-19 - Hiram) +# running simple repeat (DONE - 2020-06-12 - Hiram) mkdir /hive/data/genomes/panPan3/bed/simpleRepeat cd /hive/data/genomes/panPan3/bed/simpleRepeat time (doSimpleRepeat.pl -buildDir=`pwd` -bigClusterHub=ku \ -dbHost=hgwdev -workhorse=hgwdev -smallClusterHub=ku \ -trf409=6 panPan3) > do.log 2>&1 +XXX - running - Fri Jun 12 11:40:59 PDT 2020 # real 243m33.198s cat fb.simpleRepeat # 260449789 bases of 2999027915 (8.684%) in intersection cd /hive/data/genomes/panPan3 # using the Window Masker result: cd /hive/data/genomes/panPan3 # twoBitMask bed/windowMasker/panPan3.cleanWMSdust.2bit \ # -add bed/simpleRepeat/trfMask.bed panPan3.2bit # you can safely ignore the warning about fields >= 13 # add to rmsk after it is done: twoBitMask panPan3.rmsk.2bit \ -add bed/simpleRepeat/trfMask.bed panPan3.2bit # you can safely ignore the warning about fields >= 13 twoBitToFa panPan3.2bit stdout | faSize stdin > faSize.panPan3.2bit.txt cat faSize.panPan3.2bit.txt # 3044872214 bases (45844299 N's 2999027915 real 1490817836 upper # 1508210079 lower) in 5486 sequences in 1 files # Total size: mean 555025.9 sd 8254410.8 min 202 (chrUn_NW_022154607v1) # max 219763114 (chr1) median 29244 # %49.53 masked total, %50.29 masked real rm /gbdb/panPan3/panPan3.2bit ln -s `pwd`/panPan3.2bit /gbdb/panPan3/panPan3.2bit ######################################################################### # CREATE MICROSAT TRACK (TBD - 2019-11-20 - Hiram) ssh hgwdev mkdir /cluster/data/panPan3/bed/microsat cd /cluster/data/panPan3/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 panPan3 microsat microsat.bed # Read 27700 elements of size 4 from microsat.bed ########################################################################## ## WINDOWMASKER (TBD - 2019-11-19 - Hiram) mkdir /hive/data/genomes/panPan3/bed/windowMasker cd /hive/data/genomes/panPan3/bed/windowMasker time (doWindowMasker.pl -buildDir=`pwd` -workhorse=hgwdev \ -dbHost=hgwdev panPan3) > do.log 2>&1 # real 115m21.931s # Masking statistics cat faSize.panPan3.cleanWMSdust.txt # 3044872214 bases (45844299 N's 2999027915 real 1771826758 upper # 1227201157 lower) in 5486 sequences in 1 files # Total size: mean 555025.9 sd 8254410.8 min 202 (chrUn_NW_022154607v1) # max 219763114 (chr1) median 29244 # %40.30 masked total, %40.92 masked real cat fb.panPan3.rmsk.windowmaskerSdust.txt # 879562979 bases of 3044872214 (28.887%) in intersection ########################################################################## # cpgIslands - (TBD - 2019-11-20 - Hiram) mkdir /hive/data/genomes/panPan3/bed/cpgIslands cd /hive/data/genomes/panPan3/bed/cpgIslands time (doCpgIslands.pl -dbHost=hgwdev -bigClusterHub=ku \ -workhorse=hgwdev -smallClusterHub=ku panPan3) > do.log 2>&1 # real 4m0.657s cat fb.panPan3.cpgIslandExt.txt # 20339043 bases of 2999027915 (0.678%) in intersection ############################################################################## # genscan - (TBD - 2019-11-20 - Hiram) mkdir /hive/data/genomes/panPan3/bed/genscan cd /hive/data/genomes/panPan3/bed/genscan time (doGenscan.pl -buildDir=`pwd` -workhorse=hgwdev -dbHost=hgwdev \ -bigClusterHub=ku panPan3) > do.log 2>&1 # real 100m37.264s cat fb.panPan3.genscan.txt # 51534246 bases of 2999027915 (1.718%) in intersection cat fb.panPan3.genscanSubopt.txt # 53019930 bases of 2999027915 (1.768%) in intersection ######################################################################### # Create kluster run files (TBD - 2019-11-20 - Hiram) # numerator is panPan3 gapless bases "real" as reported by: featureBits -noRandom -noHap panPan3 gap # 41796384 bases of 2715375767 (1.539%) 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 \( 2715375767 / 2861349177 \) \* 1024 # ( 2715375767 / 2861349177 ) * 1024 = 971.760038 # ==> use -repMatch=950 according to size scaled down from 1024 for human. # and rounded down to nearest 50 cd /hive/data/genomes/panPan3 time blat panPan3.2bit \ /dev/null /dev/null -tileSize=11 -makeOoc=jkStuff/panPan3.11.ooc \ -repMatch=950 # Wrote 39217 overused 11-mers to jkStuff/panPan3.11.ooc # gorGor5 at repMatch=1100: # Wrote 31384 overused 11-mers to jkStuff/gorGor5.11.ooc # gorGor4 at repMatch=1000: # Wrote 32028 overused 11-mers to jkStuff/gorGor4.11.ooc # check non-bridged gaps to see what the typical size is: hgsql -N \ -e 'select * from gap where bridge="no" order by size;' panPan3 \ | sort -k7,7nr | ave -col=7 stdin # min 100.000000 # max 100.000000 # they are all 100 sized, 220 gaps # minimum gap size is 100 and produces a reasonable number of lifts gapToLift -verbose=2 -minGap=100 panPan3 jkStuff/panPan3.nonBridged.lft \ -bedFile=jkStuff/panPan3.nonBridged.bed wc -l jkStuff/panPan3.nonBri* # 5706 jkStuff/panPan3.nonBridged.bed # 5706 jkStuff/panPan3.nonBridged.lft ######################################################################## # lastz/chain/net swap human/hg38 (TBD - 2019-11-20 - Hiram) # original alignment cd /hive/data/genomes/hg38/bed/lastzPanPan3.2019-11-20 cat fb.hg38.chainPanPan3Link.txt # 2908900659 bases of 3095998939 (93.957%) in intersection cat fb.hg38.chainSynPanPan3Link.txt # 2885980361 bases of 3095998939 (93.216%) in intersection cat fb.hg38.chainRBest.PanPan3.txt # 2693876207 bases of 3095998939 (87.012%) in intersection # and for the swap: mkdir /hive/data/genomes/panPan3/bed/blastz.hg38.swap cd /hive/data/genomes/panPan3/bed/blastz.hg38.swap time (doBlastzChainNet.pl -verbose=2 \ /hive/data/genomes/hg38/bed/lastzPanPan3.2019-11-20/DEF \ -swap -chainMinScore=3000 -chainLinearGap=medium \ -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \ -syntenicNet) > swap.log 2>&1 # real 63m46.473s cat fb.panPan3.chainHg38Link.txt # 2738870921 bases of 2999027915 (91.325%) in intersection cat fb.panPan3.chainSynHg38Link.txt # 2728591501 bases of 2999027915 (90.983%) in intersection time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` panPan3 hg38) \ > rbest.log 2>&1 # real 62m14.470s cat fb.panPan3.chainRBest.Hg38.txt # 2697792568 bases of 2999027915 (89.956%) in intersection ########################################################################### # lastz/chain/net swap mouse/mm10 (TBD - 2019-11-21 - Hiram) # original alignment cd /hive/data/genomes/mm10/bed/lastzPanPan3.2019-11-20 cat fb.mm10.chainPanPan3Link.txt # 929953885 bases of 2652783500 (35.056%) in intersection cat fb.mm10.chainSynPanPan3Link.txt # 882047357 bases of 2652783500 (33.250%) in intersection cat fb.mm10.chainRBest.PanPan3.txt # 885135149 bases of 2652783500 (33.366%) in intersection mkdir /hive/data/genomes/panPan3/bed/blastz.mm10.swap cd /hive/data/genomes/panPan3/bed/blastz.mm10.swap time (doBlastzChainNet.pl -verbose=2 \ /hive/data/genomes/mm10/bed/lastzPanPan3.2019-11-20/DEF \ -swap -syntenicNet \ -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \ -chainMinScore=3000 -chainLinearGap=medium) > swap.log 2>&1 # real 72m34.088s cat fb.panPan3.chainMm10Link.txt # 1017872526 bases of 2999027915 (33.940%) in intersection cat fb.panPan3.chainSynMm10Link.txt # 880983055 bases of 2999027915 (29.376%) in intersection time (doRecipBest.pl -load -workhorse=hgwdev panPan3 mm10 \ -buildDir=`pwd` -workhorse=hgwdev) > rbest.log 2>&1 & # real 237m38.959s cat fb.panPan3.chainRBest.Mm10.txt # 883663662 bases of 2999027915 (29.465%) in intersection ############################################################################## # GENBANK AUTO UPDATE (TBD - 2019-11-20 - Hiram) ssh hgwdev cd $HOME/kent/src/hg/makeDb/genbank git pull # /cluster/data/genbank/data/organism.lst shows: # organism mrnaCnt estCnt refSeqCnt # Gorilla 1 0 0 # Gorilla gorilla 617 30 95 # Gorilla gorilla gorilla 4 0 0 # that single 'Gorilla' name is a new one, adding that to # the list of Gorilla names in src/lib/gbGenome.c # edit etc/genbank.conf to add panPan3 just before galGal5 # Gorilla - refseq assembly: GCF_008122165.1 panPan3.serverGenome = /hive/data/genomes/panPan3/panPan3.2bit panPan3.ooc = /hive/data/genomes/panPan3/jkStuff/panPan3.11.ooc panPan3.lift = /hive/data/genomes/panPan3/jkStuff/panPan3.nonBridged.lft panPan3.perChromTables = no panPan3.refseq.mrna.native.pslCDnaFilter = ${ordered.refseq.mrna.native.pslCDnaFilter} panPan3.refseq.mrna.xeno.pslCDnaFilter = ${ordered.refseq.mrna.xeno.pslCDnaFilter} panPan3.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter} panPan3.genbank.mrna.xeno.pslCDnaFilter = ${ordered.genbank.mrna.xeno.pslCDnaFilter} panPan3.genbank.est.native.pslCDnaFilter = ${ordered.genbank.est.native.pslCDnaFilter} panPan3.genbank.est.xeno.pslCDnaFilter = ${ordered.genbank.est.xeno.pslCDnaFilter} panPan3.downloadDir = panPan3 # default yes refseq.mrna.native refseq.mrna.xeno genbank.mrna.native # default yes genbank.est.native # default no genbank.mrna.xeno genbank.est.xeno # verify the files specified exist before checking in the file: grep ^panPan3 etc/genbank.conf | grep hive | awk '{print $NF}' | xargs ls -og # -rw-rw-r-- 1 792944027 Nov 20 10:59 /hive/data/genomes/panPan3/panPan3.2bit # -rw-rw-r-- 1 156876 Nov 20 11:06 /hive/data/genomes/panPan3/jkStuff/panPan3.11.ooc # -rw-rw-r-- 1 333597 Nov 20 11:08 /hive/data/genomes/panPan3/jkStuff/panPan3.nonBridged.lft git commit -m "Added panPan3 gorilla; refs #24524" etc/genbank.conf src/lib/gbGenome.c git push # update the binaries due to the update in lib/src/gbGenome.c make install-server # update /cluster/data/genbank/: make etc-update # enable daily alignment and update of hgwdev cd ~/kent/src/hg/makeDb/genbank git pull # add panPan3 to: # etc/hgwdev.dbs etc/align.dbs git commit -m "Added panPan3 - gorilla refs #24524" etc/hgwdev.dbs etc/align.dbs git push make etc-update # wait a few days for genbank magic to take place, the tracks will # appear ############################################################################# # augustus gene track (TBD - 2019-11-20 - Hiram) mkdir /hive/data/genomes/panPan3/bed/augustus cd /hive/data/genomes/panPan3/bed/augustus time (doAugustus.pl -buildDir=`pwd` -bigClusterHub=ku \ -species=human -dbHost=hgwdev \ -workhorse=hgwdev panPan3) > do.log 2>&1 # real 139m55.244s cat fb.panPan3.augustusGene.txt # 55005426 bases of 2999027915 (1.834%) in intersection ######################################################################### # ncbiRefSeq (TBD - 2019-11-20 - Hiram) mkdir /hive/data/genomes/panPan3/bed/ncbiRefSeq cd /hive/data/genomes/panPan3/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 Gorilla_gorilla \ GCF_008122165.1_Kamilah_GGO_v0 panPan3) > download.log 2>&1 # real 1m37.523s 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 Gorilla_gorilla \ GCF_008122165.1_Kamilah_GGO_v0 panPan3) > process.log 2>&1 # real 2m9.450s 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 Gorilla_gorilla \ GCF_008122165.1_Kamilah_GGO_v0 panPan3) > load.log 2>&1 # real 0m21.982s cat fb.ncbiRefSeq.panPan3.txt # 74279781 bases of 2999027915 (2.477%) in intersection # add: include ../../refSeqComposite.ra alpha # to the gorilla/panPan3/trackDb.ra to turn on the track in the browser featureBits -enrichment panPan3 refGene ncbiRefSeq # refGene 0.006%, ncbiRefSeq 2.477%, both 0.006%, cover 99.87%, enrich 40.32x featureBits -enrichment panPan3 ncbiRefSeq refGene # ncbiRefSeq 2.477%, refGene 0.006%, both 0.006%, cover 0.25%, enrich 40.32x featureBits -enrichment panPan3 ncbiRefSeqCurated refGene # ncbiRefSeqCurated 0.007%, refGene 0.006%, both 0.006%, cover 94.29%, enrich 14956.14x featureBits -enrichment panPan3 refGene ncbiRefSeqCurated # refGene 0.006%, ncbiRefSeqCurated 0.007%, both 0.006%, cover 99.87%, enrich 14956.14x ######################################################################### # LIFTOVER TO gorGor5 (TBD - 2019-11-20 - Hiram) ssh hgwdev mkdir /hive/data/genomes/panPan3/bed/blat.gorGor5.2019-11-20 cd /hive/data/genomes/panPan3/bed/blat.gorGor5.2019-11-20 doSameSpeciesLiftOver.pl -verbose=2 \ -debug -bigClusterHub=ku -dbHost=hgwdev -workhorse=hgwdev \ -ooc=/hive/data/genomes/panPan3/jkStuff/panPan3.11.ooc \ panPan3 gorGor5 time (doSameSpeciesLiftOver.pl -verbose=2 \ -bigClusterHub=ku -dbHost=hgwdev -workhorse=hgwdev \ -ooc=/hive/data/genomes/panPan3/jkStuff/panPan3.11.ooc \ panPan3 gorGor5) > doLiftOverToGorGor5.log 2>&1 # real 936m35.524s # see if the liftOver menus function in the browser from panPan3 to gorGor5 ######################################################################### # LIFTOVER TO gorGor4 (TBD - 2019-11-20 - Hiram) ssh hgwdev mkdir /hive/data/genomes/panPan3/bed/blat.gorGor4.2019-11-20 cd /hive/data/genomes/panPan3/bed/blat.gorGor4.2019-11-20 doSameSpeciesLiftOver.pl -verbose=2 \ -debug -bigClusterHub=ku -dbHost=hgwdev -workhorse=hgwdev \ -ooc=/hive/data/genomes/panPan3/jkStuff/panPan3.11.ooc \ panPan3 gorGor4 time (doSameSpeciesLiftOver.pl -verbose=2 \ -bigClusterHub=ku -dbHost=hgwdev -workhorse=hgwdev \ -ooc=/hive/data/genomes/panPan3/jkStuff/panPan3.11.ooc \ panPan3 gorGor4) > doLiftOverToGorGor4.log 2>&1 # real 654m46.645s # see if the liftOver menus function in the browser from panPan3 to gorGor4 ######################################################################### # BLATSERVERS ENTRY (TBD - 2019-11-20 - 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 ("panPan3", "blat1c", "17914", "1", "0"); \ INSERT INTO blatServers (db, host, port, isTrans, canPcr) \ VALUES ("panPan3", "blat1c", "17915", "0", "1");' \ hgcentraltest # test it with some sequence ############################################################################ ## reset default position similar to gorGor5 found via blat of NR_046473.1 mRNA ## (TBD - 2019-11-20 - Hiram) # as found from the galGal5 to panPan3 liftOver ssh hgwdev hgsql -e 'update dbDb set defaultPos="chr14:81559118-81601404" where name="panPan3";' hgcentraltest ############################################################################## # crispr whole genome (TBD - 2019-11-20 - Hiram) mkdir /hive/data/genomes/panPan3/bed/crisprAll cd /hive/data/genomes/panPan3/bed/crisprAll # the large shoulder argument will cause the entire genome to be scanned # this takes a while for a new genome to get the bwa indexing done time (~/kent/src/hg/utils/automation/doCrispr.pl -verbose=2 -stop=ranges \ panPan3 ncbiRefSeq -shoulder=250000000 -tableName=crisprAll -fileServer=hgwdev \ -buildDir=`pwd` -smallClusterHub=hgwdev -bigClusterHub=ku \ -workhorse=hgwdev) > ranges.log 2>&1 # real 72m58.740s time (~/kent/src/hg/utils/automation/doCrispr.pl -verbose=2 \ -continue=guides -stop=specScores panPan3 ncbiRefSeq \ -shoulder=250000000 -tableName=crisprAll -fileServer=hgwdev \ -buildDir=`pwd` -smallClusterHub=hgwdev -bigClusterHub=ku \ -workhorse=hgwdev) > specScores.log 2>&1 # real 8m40.172s cat guides/run.time | sed -e 's/^/# /;' # Completed: 100 of 100 jobs # CPU time in finished jobs: 12309s 205.15m 3.42h 0.14d 0.000 y # IO & Wait Time: 290s 4.83m 0.08h 0.00d 0.000 y # Average job time: 126s 2.10m 0.03h 0.00d # Longest finished job: 380s 6.33m 0.11h 0.00d # Submission to last job: 386s 6.43m 0.11h 0.00d cat specScores/run.time | sed -e 's/^/# /;' # Completed: 3041114 of 3041114 jobs # CPU time in finished jobs: 282305886s 4705098.10m 78418.30h 3267.43d 8.952 y # IO & Wait Time: 84009113s 1400151.88m 23335.86h 972.33d 2.664 y # Average job time: 120s 2.01m 0.03h 0.00d # Longest finished job: 498s 8.30m 0.14h 0.01d # Submission to last job: 381920s 6365.33m 106.09h 4.42d Submission to last job: 274925s 4582.08m 76.37h 3.18d # Number of specScores: 227564780 # real 7482m37.507s # user 0m2.047s # sys 0m2.110s ### remember to get back to hgwdev to run this time (~/kent/src/hg/utils/automation/doCrispr.pl -verbose=2 \ -continue=effScores -stop=load panPan3 ncbiRefSeq \ -shoulder=250000000 -tableName=crisprAll -fileServer=hgwdev \ -buildDir=`pwd` -smallClusterHub=hgwdev -bigClusterHub=ku \ -workhorse=hgwdev) > load.log 2>&1 # real 1081m16.460s cat effScores/run.time | sed -e 's/^/# /;' # Completed: 27933 of 27933 jobs # CPU time in finished jobs: 13825593s 230426.55m 3840.44h 160.02d 0.438 y # IO & Wait Time: 172582s 2876.37m 47.94h 2.00d 0.005 y # Average job time: 501s 8.35m 0.14h 0.01d # Longest finished job: 20199s 336.65m 5.61h 0.23d # Submission to last job: 22274s 371.23m 6.19h 0.26d cat offTargets/run.time | sed -e 's/^/# /;' # Completed: 152056 of 152056 jobs # CPU time in finished jobs: 2009038s 33483.97m 558.07h 23.25d 0.064 y # IO & Wait Time: 2321685s 38694.75m 644.91h 26.87d 0.074 y # Average job time: 28s 0.47m 0.01h 0.00d # Longest finished job: 53s 0.88m 0.01h 0.00d # Submission to last job: 4266s 71.10m 1.19h 0.05d ######################################################################### # all.joiner update, downloads and in pushQ - (WORKING - 2019-11-20 - Hiram) cd $HOME/kent/src/hg/makeDb/schema # verify all the business is done for release ~/kent/src/hg/utils/automation/verifyBrowser.pl panPan3 # fixup all.joiner until this is a clean output joinerCheck -database=panPan3 -tableCoverage all.joiner joinerCheck -database=panPan3 -times all.joiner joinerCheck -database=panPan3 -keys all.joiner # when clean, check in: git commit -m 'adding rules for panPan3 refs #24524' all.joiner git push # run up a 'make alpha' in hg/hgTables to get this all.joiner file # into the hgwdev/genome-test system cd /hive/data/genomes/panPan3 time (~/kent/src/hg/utils/automation/makeDownloads.pl panPan3) > downloads.log 2>&1 # real 17m56.213s XXX - ready to continue - Tue Mar 31 14:27:51 PDT 2020 # now ready for pushQ entry mkdir /hive/data/genomes/panPan3/pushQ cd /hive/data/genomes/panPan3/pushQ time ($HOME/kent/src/hg/utils/automation/makePushQSql.pl -redmineList panPan3) > panPan3.pushQ.sql 2> stderr.out # real 15m52.548s # remove the tandemDups and gapOverlap from the file list: sed -i -e "/tandemDups/d" redmine.panPan3.table.list sed -i -e "/Tandem Dups/d" redmine.panPan3.releaseLog.txt sed -i -e "/gapOverlap/d" redmine.panPan3.table.list sed -i -e "/Gap Overlaps/d" redmine.panPan3.releaseLog.txt # check for errors in stderr.out, some are OK, e.g.: # WARNING: hgwdev does not have /gbdb/panPan3/wib/gc5Base.wib # WARNING: hgwdev does not have /gbdb/panPan3/wib/quality.wib # WARNING: hgwdev does not have /gbdb/panPan3/bbi/quality.bw # WARNING: panPan3 does not have seq # WARNING: panPan3 does not have extFile # verify the file list does correctly match to files cat redmine.panPan3.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.panPan3.table.list # 63 redmine.panPan3.table.list # how many actual: awk -F'.' '{printf "hgsql -N %s -e '"'"'show table status like \"%s\";'"'"'\n", $1, $2}' redmine.panPan3.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/panPan3/pushQ/redmine.panPan3.file.list # /hive/data/genomes/panPan3/pushQ/redmine.panPan3.releaseLog.txt # /hive/data/genomes/panPan3/pushQ/redmine.panPan3.table.list #########################################################################