# for emacs: -*- mode: sh; -*- # This file describes browser build for the criGriChoV1 ######################################################################### # micrograph photograph from WikiMedia cell lines # (DONE - 2017-03-27 - Hiram) mkdir -p /hive/data/genomes/criGriChoV1/photo cd /hive/data/genomes/criGriChoV1/photo wget --timestamping \ https://upload.wikimedia.org/wikipedia/commons/5/54/Cho_cells_adherend2.jpg convert -quality 80 -geometry 300x300 Cho_cells_adherend2.jpg criGriChoV1.jpg printf 'photoCreditURL https://commons.wikimedia.org/wiki/File:Cho_cells_adherend2.jpg photoCreditName WikiMedia Commons: Alcibiades ' > photoReference.txt cat photoReference.txt photoCreditURL https://commons.wikimedia.org/wiki/File:Cho_cells_adherend2.jpg photoCreditName WikiMedia Commons: Alcibiades # Checking in that photograph to the source tree, will need to fixup the # description.html page to correctly reference this photo ######################################################################### # Initial steps (DONE - 2017-04-11 - Hiram) # To start this initialBuild.txt document, from a previous assembly document: mkdir ~/kent/src/hg/makeDb/doc/criGriChoV1 cd ~/kent/src/hg/makeDb/doc/criGriChoV1 # best to use a most recent document since it has the latest features and # procedures: sed -e 's/xenTro9/criGriChoV1/g; s/XenTro9/CriGriChoV1/g; s/DONE/TBD/g;' ../xenTro9/initialBuild.txt > initialBuild.txt mkdir /hive/data/genomes/criGriChoV1/refseq cd /hive/data/genomes/criGriChoV1/refseq time rsync -L -a -P \ rsync://ftp.ncbi.nlm.nih.gov/genomes/refseq/vertebrate_mammalian/Cricetulus_griseus/all_assembly_versions/GCF_000223135.1_CriGri_1.0/ ./ # sent 562 bytes received 2737626948 bytes 23498948.58 bytes/sec # total size is 2737289916 speedup is 1.00 # real 1m55.945s # check assembly size for later reference: faSize G*_1.0_genomic.fna.gz # 2399786748 bases (81654506 N's 2318132242 real 1610008392 upper # 708123850 lower) in 109152 sequences in 1 files # Total size: mean 21985.7 sd 185816.1 min 200 (NW_003722730.1) # max 8779783 (NW_003613580.1) median 503 # %29.51 masked total, %30.55 masked real # this information is from the top of # criGriChoV1/refseq/GCF_000223135.1_CriGri_1.0_assembly_report.txt # Assembly name: CriGri_1.0 # Description: Genome assembly from the chinese hamster ovary cell line CHO-K1 # Organism name: Cricetulus griseus (Chinese hamster) # Taxid: 10029 # BioSample: SAMN02981352 # BioProject: PRJNA69991 # Submitter: Beijing Genomics Institute # Date: 2011-8-23 # Assembly type: haploid # Release type: major # Assembly level: Scaffold # Genome representation: full # WGS project: AFTD01 # Assembly method: SOAPdenovo v. 1.05 # Genome coverage: 130x # Sequencing technology: Illumina GA IIx # RefSeq category: Representative Genome # GenBank assembly accession: GCA_000223135.1 # RefSeq assembly accession: GCF_000223135.1 # RefSeq assembly and GenBank assemblies identical: no # ## Assembly-Units: ## GenBank Unit Accession RefSeq Unit Accession Assembly-Unit name ## GCA_000223145.1 GCF_000223145.1 Primary Assembly ## GCF_000055695.1 non-nuclear ############################################################################# # establish config.ra file (DONE - Hiram - 2017-04-11) # arguments here are: cd /hive/data/genomes/criGriChoV1 $HOME/kent/src/hg/utils/automation/prepConfig.pl criGriChoV1 mammal \ criGri ./refseq/*_assembly_report.txt > criGriChoV1.config.ra # fixup assemblyShortLabel # to see order keys to verify this one is correct: # hgsql -e 'select name,organism,orderKey from dbDb order by orderKey;' \ # hgcentraltest | less # verify it looks sane cat criGriChoV1.config.ra # config parameters for makeGenomeDb.pl: db criGriChoV1 clade mammal scientificName Cricetulus griseus commonName Chinese hamster assemblyDate Aug. 2011 assemblyLabel Beijing Genomics Institute assemblyShortLabel CHO K1 cell line orderKey 3349 # mitochondrial sequence included in refseq release # mitoAcc NC_007936.1 mitoAcc none fastaFiles /hive/data/genomes/criGriChoV1/ucsc/*.fa.gz agpFiles /hive/data/genomes/criGriChoV1/ucsc/*.agp # qualFiles none dbDbSpeciesDir criGri photoCreditURL https://commons.wikimedia.org/wiki/File:Cho_cells_adherend2.jpg photoCreditName WikiMedia Commons: Alcibiades ncbiGenomeId 2791 ncbiAssemblyId 309608 ncbiAssemblyName CriGri_1.0 ncbiBioProject 69991 ncbiBioSample SAMN02981352 genBankAccessionID GCF_000223135.1 taxId 10029 ############################################################################# # setup UCSC named files (DONE - 2017-04-11 - Hiram) mkdir /hive/data/genomes/criGriChoV1/ucsc cd /hive/data/genomes/criGriChoV1/ucsc # check for duplicate sequences: time faToTwoBit -noMask ../refseq/G*_1.0_genomic.fna.gz refseq.2bit # real 0m59.891s 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 # note: mitochondrial sequence in this assembly: NC_007936.1 # unplaced scaffold assembly merely needs the .1 names changed to v1 # and since there are all .1 versions, this sed statement will make them # all v1 version names: zcat ../refseq/GCF_000223135.1_CriGri_1.0_assembly_structure/Primary_Assembly/unplaced_scaffolds/AGP/unplaced.scaf.agp.gz \ | grep -v "^#" | sed -e 's/\.1/v1/;' > chrUn.criGriChoV1.agp zcat ../refseq/GCF_000223135.1_CriGri_1.0_assembly_structure/Primary_Assembly/unplaced_scaffolds/FASTA/unplaced.scaf.fna.gz \ | sed -e 's/.1 Cricetulus .*/v1/;' | gzip -c > chrUn.criGriChoV1.fa.gz # bash syntax here mitoAcc=`grep "^# mitoAcc" ../criGriChoV1.config.ra | awk '{print $NF}'` printf "# mitoAcc %s\n" "$mitoAcc" # mitoAcc NC_007936.1 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 1m5.661s time cat *.agp | checkAgpAndFa stdin test.2bit 2>&1 | tail -4 # Valid Fasta file entry # All AGP and FASTA entries agree - both files are valid # real 1m20.989s # and no sequence lost from orginal: twoBitToFa test.2bit stdout | faSize stdin # 2399786748 bases (81654506 N's 2318132242 real 2318132242 upper 0 lower) # in 109152 sequences in 1 files # Total size: mean 21985.7 sd 185816.1 min 200 (NW_003722730v1) # max 8779783 (NW_003613580v1) median 503 # same numbers as above # 2399786748 bases (81654506 N's 2318132242 real 1610008392 upper # 708123850 lower) in 109152 sequences in 1 files # Total size: mean 21985.7 sd 185816.1 min 200 (NW_003722730.1) # max 8779783 (NW_003613580.1) median 503 # no longer need these temporary 2bit files rm refseq.2bit test.2bit ############################################################################# # Initial database build (DONE - 2017-04-11 - Hiram) cd /hive/data/genomes/criGriChoV1 # verify sequence and AGP are OK: time (makeGenomeDb.pl -workhorse=hgwdev -dbHost=hgwdev -fileServer=hgwdev \ -stop=agp criGriChoV1.config.ra) > agp.log 2>&1 # real 3m50.363s # then finish it off: time (makeGenomeDb.pl -workhorse=hgwdev -dbHost=hgwdev \ -fileServer=hgwdev -continue=db criGriChoV1.config.ra) > db.log 2>&1 # real 21m36.451s # check in the trackDb files created in TemporaryTrackDbCheckout/ # and add criGriChoV1 to trackDb/makefile # temporary symlink until masked sequence is available cd /hive/data/genomes/criGriChoV1 ln -s `pwd`/criGriChoV1.unmasked.2bit /gbdb/criGriChoV1/criGriChoV1.2bit ############################################################################## # cpgIslands on UNMASKED sequence (DONE - 2017-04-11 - Hiram) mkdir /hive/data/genomes/criGriChoV1/bed/cpgIslandsUnmasked cd /hive/data/genomes/criGriChoV1/bed/cpgIslandsUnmasked time (doCpgIslands.pl -dbHost=hgwdev -bigClusterHub=ku -buildDir=`pwd` \ -tableName=cpgIslandExtUnmasked \ -maskedSeq=/hive/data/genomes/criGriChoV1/criGriChoV1.unmasked.2bit \ -workhorse=hgwdev -smallClusterHub=ku criGriChoV1) > do.log 2>&1 # real 23m21.863s cat fb.criGriChoV1.cpgIslandExtUnmasked.txt # 6108135 bases of 2318132242 (0.263%) in intersection ############################################################################# # cytoBandIdeo - (DONE - 2017-04-11 - Hiram) mkdir /hive/data/genomes/criGriChoV1/bed/cytoBand cd /hive/data/genomes/criGriChoV1/bed/cytoBand makeCytoBandIdeo.csh criGriChoV1 ######################################################################### # ucscToINSDC and ucscToRefSeq table/track (DONE - 2017-04-11 - 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/criGriChoV1/bed/ucscToINSDC cd /hive/data/genomes/criGriChoV1/bed/ucscToINSDC # find accession for chrM grep chrM ../../criGriChoV1.agp # chrM 1 16284 1 O NC_007936.1 1 16284 + # find the genbank accession for NC_007936.1 at Entrez nucleotide # The NC_007936.1 name is the RefSeq name, the genbank name is: DQ390542.2 # the assembly_report does not have this AY name since the chrM sequence # is not in the genbank assembly: grep NC_007936.1 ../../refseq/GCF*_1.0_assembly_report.txt # MT assembled-molecule MT Mitochondrion na <> NC_007936.1 non-nuclear 16284 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_007936.1 # this is actually ucscToRefSeq since this is a RefSeq assembly sort -k2 ucscToINSDC.txt > ucscToRefSeq.txt rm -f ucscToINSDC.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/DQ390542.2/' \ | 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 # chrM is already there # printf "chrM\t0\t16284\tNC_007936.1\n" >> 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 # chrM is already there # printf "chrM\t0\t16284\tDQ390542.2\n" >> ucscToINSDC.bed # verify chrM is correct: grep chrM *.bed # ucscToINSDC.bed:chrM 0 16284 DQ390542.2 # ucscToRefSeq.bed:chrM 0 16284 NC_007936.1 # 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 * # 109152 refSeqToUcsc.txt # 109152 refseq.insdc.txt # 109152 ucsc.coordinate.tab # 109152 ucscToINSDC.bed # 109152 ucscToRefSeq.bed # 109152 ucscToRefSeq.txt export chrSize=`cut -f1 ucscToINSDC.bed | awk '{print length($0)}' | sort -n | tail -1` echo $chrSize # 14 # use the chrSize in this sed sed -e "s/21/$chrSize/" $HOME/kent/src/hg/lib/ucscToINSDC.sql \ | hgLoadSqlTab criGriChoV1 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 $chrSize # 14 sed -e "s/21/$chrSize/" $HOME/kent/src/hg/lib/ucscToINSDC.sql \ | sed -e 's/INSDC/RefSeq/g;' > ucscToRefSeq.sql hgLoadSqlTab criGriChoV1 ucscToRefSeq ./ucscToRefSeq.sql ucscToRefSeq.bed # checkTableCoords should be silent checkTableCoords criGriChoV1 # each should cover %100 entirely: featureBits -countGaps criGriChoV1 ucscToINSDC # 2399786748 bases of 2399786748 (100.000%) in intersection featureBits -countGaps criGriChoV1 ucscToRefSeq # 2399786748 bases of 2399786748 (100.000%) in intersection ######################################################################### # add chromAlias table (DONE - 2017-04-11 - Hiram) mkdir /hive/data/genomes/criGriChoV1/bed/chromAlias cd /hive/data/genomes/criGriChoV1/bed/chromAlias hgsql -N -e 'select chrom,name,"refseq" from ucscToRefSeq;' criGriChoV1 \ > ucsc.refseq.tab hgsql -N -e 'select chrom,name,"genbank" from ucscToINSDC;' criGriChoV1 \ > ucsc.genbank.tab awk '{printf "%s\t%s\t%s\n", $2,$1,$3}' ucsc.genbank.tab ucsc.refseq.tab \ | sort > criGriChoV1.chromAlias.tab hgLoadSqlTab criGriChoV1 chromAlias ~/kent/src/hg/lib/chromAlias.sql \ criGriChoV1.chromAlias.tab ######################################################################### # fixup search rule for assembly track/gold table (DONE - 2017-04-11 - Hiram) cd ~/kent/src/hg/makeDb/trackDb/criGri/criGriChoV1 # preview prefixes and suffixes: hgsql -N -e "select frag from gold;" criGriChoV1 \ | sed -e 's/[0-9][0-9]*//;' | sort | uniq -c # 265786 AFTD.1 # 1 NC_.1 # implies a rule: '[AN][CF][T_][D0-9]+(\.[0-9]+)?' # verify this rule will find them all and eliminate them all: hgsql -N -e "select frag from gold;" criGriChoV1 | wc -l # 265787 hgsql -N -e "select frag from gold;" criGriChoV1 \ | egrep -e '[AN][CF][T_][D0-9]+(\.[0-9]+)?' | wc -l # 265787 hgsql -N -e "select frag from gold;" criGriChoV1 \ | egrep -v -e '[AN][CF][T_][D0-9]+(\.[0-9]+)?' | wc -l # 0 # hence, add to trackDb/chicken/criGriChoV1/trackDb.ra searchTable gold shortCircuit 1 termRegex [AN][CF][T_][D0-9]+(\.[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 - 2017-04-11 - Hiram) mkdir /hive/data/genomes/criGriChoV1/bed/repeatMasker cd /hive/data/genomes/criGriChoV1/bed/repeatMasker time (doRepeatMasker.pl -buildDir=`pwd` \ -bigClusterHub=ku -dbHost=hgwdev -workhorse=hgwdev \ -smallClusterHub=ku criGriChoV1) > do.log 2>&1 & # there were difficulties with some jobs, they appeared to be making # no progress after several days. They were killed on their ku nodes # and allowed to continue. They then finished normally. # real 2066m40.189s cat faSize.rmsk.txt # 2399786748 bases (81654506 N's 2318132242 real 1661086119 upper # 657046123 lower) in 109152 sequences in 1 files # Total size: mean 21985.7 sd 185816.1 min 200 (NW_003722730v1) # max 8779783 (NW_003613580v1) median 503 # %27.38 masked total, %28.34 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 criGriChoV1 rmsk # 658545363 bases of 2399786748 (27.442%) in intersection # real 0m59.195s # 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;' criGriChoV1 \ | bedSingleCover.pl stdin | ave -col=4 stdin | grep "^total" # total 658545363.000000 # real 0m30.646s ########################################################################## # running simple repeat (DONE - 2017-04-11 - Hiram) mkdir /hive/data/genomes/criGriChoV1/bed/simpleRepeat cd /hive/data/genomes/criGriChoV1/bed/simpleRepeat # using trf409 6 here (human == 6) time (doSimpleRepeat.pl -buildDir=`pwd` -bigClusterHub=ku \ -dbHost=hgwdev -workhorse=hgwdev -smallClusterHub=ku \ -trf409 6 criGriChoV1) > do.log 2>&1 & # real 53m53.100s cat fb.simpleRepeat # 118499828 bases of 1369865365 (8.650%) in intersection # in this case, and given previous experience with criGri1, # is isn't good enough to use just RM or WM, they need to # be added together. # adding this trfMask to the other masking cd /hive/data/genomes/criGriChoV1 # when using Rmsk results, add to rmsk after it is done: twoBitMask criGriChoV1.rmsk.2bit \ -add bed/simpleRepeat/trfMask.bed criGriChoV1.rmsk.trf.2bit # you can safely ignore the warning about fields >= 13 twoBitToFa criGriChoV1.rmsk.trf.2bit stdout | faSize stdin # 2399786748 bases (81654506 N's 2318132242 real 1659593917 upper # 658538325 lower) in 109152 sequences in 1 files # Total size: mean 21985.7 sd 185816.1 min 200 (NW_003722730v1) # max 8779783 (NW_003613580v1) median 503 # %27.44 masked total, %28.41 masked real # adding the Window Masker result: twoBitMask criGriChoV1.rmsk.trf.2bit \ -type=.bed -add bed/windowMasker/cleanWMask.bed.gz criGriChoV1.2bit # you can safely ignore the warning about fields >= 13 twoBitMask -type=.bed bed/windowMasker/criGriChoV1.cleanWMSdust.2bit \ -add bed/simpleRepeat/trfMask.bed criGriChoV1.WM.trf.2bit twoBitToFa criGriChoV1.2bit stdout \ | faSize stdin > faSize.criGriChoV1.2bit.txt cat faSize.criGriChoV1.2bit.txt # 2399786748 bases (81654506 N's 2318132242 real 1302163828 upper # 1015968414 lower) in 109152 sequences in 1 files # Total size: mean 21985.7 sd 185816.1 min 200 (NW_003722730v1) # max 8779783 (NW_003613580v1) median 503 # %42.34 masked total, %43.83 masked real # reset the symlink rm /gbdb/criGriChoV1/criGriChoV1.2bit ln -s `pwd`/criGriChoV1.2bit /gbdb/criGriChoV1/criGriChoV1.2bit ######################################################################### # CREATE MICROSAT TRACK (DONE - 2017-04-11 - Hiram) ssh hgwdev mkdir /cluster/data/criGriChoV1/bed/microsat cd /cluster/data/criGriChoV1/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 criGriChoV1 microsat microsat.bed # Read 213828 elements of size 4 from microsat.bed ########################################################################## ## WINDOWMASKER (DONE - 2017-04-11 - Hiram) mkdir /hive/data/genomes/criGriChoV1/bed/windowMasker cd /hive/data/genomes/criGriChoV1/bed/windowMasker time (doWindowMasker.pl -buildDir=`pwd` -workhorse=hgwdev \ -dbHost=hgwdev criGriChoV1) > do.log 2>&1 # real 299m17.427s # finished before RepeatMasker, failed on featureBits rmsk, so finish # this off time (doWindowMasker.pl -buildDir=`pwd` -workhorse=hgwdev \ -continue=cleanup -dbHost=hgwdev criGriChoV1) > cleanup.log 2>&1 # Masking statistics cat faSize.criGriChoV1.cleanWMSdust.txt # 2399786748 bases (81654506 N's 2318132242 real 1597264069 upper # 720868173 lower) in 109152 sequences in 1 files # Total size: mean 21985.7 sd 185816.1 min 200 (NW_003722730v1) # max 8779783 (NW_003613580v1) median 503 # %30.04 masked total, %31.10 masked real cat fb.criGriChoV1.rmsk.windowmaskerSdust.txt # 362147143 bases of 2399786748 (15.091%) in intersection # check to see what the addition together would be # for rmsk and WM: featureBits -or -countGaps criGriChoV1 rmsk windowmaskerSdust \ > fb.criGriChoV1.rmsk+windowmaskerSdust.txt 2>&1 cat fb.criGriChoV1.rmsk+windowmaskerSdust.txt # 1017266393 bases of 2399786748 (42.390%) in intersection ########################################################################## # run up idKeys files for ncbiRefSeq (DONE - 2017-04-13 - Hiram) mkdir /hive/data/genomes/criGriChoV1/bed/idKeys cd /hive/data/genomes/criGriChoV1/bed/idKeys time (doIdKeys.pl -buildDir=`pwd` criGriChoV1) > do.log 2>&1 & # real 45m2.374s cat criGriChoV1.keySignature.txt # 832a66e945d9edd075787c256aedfae0 ########################################################################## # cpgIslands - (DONE - 2017-04-13 - Hiram) mkdir /hive/data/genomes/criGriChoV1/bed/cpgIslands cd /hive/data/genomes/criGriChoV1/bed/cpgIslands time (doCpgIslands.pl -dbHost=hgwdev -bigClusterHub=ku \ -workhorse=hgwdev -smallClusterHub=ku criGriChoV1) > do.log 2>&1 & # real 10m43.281s cat fb.criGriChoV1.cpgIslandExt.txt # 4837862 bases of 2318132242 (0.209%) in intersection ############################################################################## # genscan - (DONE - 2017-04-13 - Hiram) mkdir /hive/data/genomes/criGriChoV1/bed/genscan cd /hive/data/genomes/criGriChoV1/bed/genscan time (doGenscan.pl -buildDir=`pwd` -workhorse=hgwdev -dbHost=hgwdev \ -bigClusterHub=ku criGriChoV1) > do.log 2>&1 & # real 65m50.006s cat fb.criGriChoV1.genscan.txt # 31211644 bases of 2318132242 (1.346%) in intersection cat fb.criGriChoV1.genscanSubopt.txt # 37035688 bases of 2318132242 (1.598%) in intersection ############################################################################# # augustus gene track (DONE - 2017-04-13 - Hiram) mkdir /hive/data/genomes/criGriChoV1/bed/augustus cd /hive/data/genomes/criGriChoV1/bed/augustus time (doAugustus.pl -buildDir=`pwd` -bigClusterHub=ku \ -species=human -dbHost=hgwdev -workhorse=hgwdev criGriChoV1) > do.log 2>&1 & # real 72m23.671s cat fb.criGriChoV1.augustusGene.txt # 29811614 bases of 2318132242 (1.286%) in intersection ######################################################################### # LIFTOVER TO criGri1 (DONE - 2017-04-13 - Hiram) ssh hgwdev mkdir /hive/data/genomes/criGriChoV1/bed/blat.criGri1.2017-04-13 cd /hive/data/genomes/criGriChoV1/bed/blat.criGri1.2017-04-13 time (doSameSpeciesLiftOver.pl -verbose=2 -buildDir=`pwd` \ -ooc=/hive/data/genomes/criGriChoV1/jkStuff/criGriChoV1.11.ooc \ -bigClusterHub=ku -dbHost=hgwdev -workhorse=hgwdev \ criGriChoV1 criGri1) > do.log 2>&1 & # real 1589m33.139s # verify the convert link on the test browser is now active # from criGriChoV1 to criGri1 ############################################################################# # SWAP lastz/chain/net criGriChoV1 (DONE - 2017-04-24 - Hiram) # this is in addition to the blat liftOver result, not to # replace that result, but just to get this chainNet track on the # browser which the blat liftOver does not create. # alignment to criGri1 cd /hive/data/genomes/criGri1/bed/lastzCriGriChoV1.2017-04-19 cat fb.criGri1.chainCriGriChoV1Link.txt # 2258183039 bases of 2301325917 (98.125%) in intersection # and for the swap: mkdir /hive/data/genomes/criGriChoV1/bed/blastz.criGri1.swap cd /hive/data/genomes/criGriChoV1/bed/blastz.criGri1.swap # stop at 'load' to avoid changing liftOver (already done with blat) time (doBlastzChainNet.pl -verbose=2 \ /hive/data/genomes/criGri1/bed/lastzCriGriChoV1.2017-04-19/DEF \ -swap -chainMinScore=1000 -chainLinearGap=loose \ -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \ -stop=load -noDbNameCheck -syntenicNet) > swap.log 2>&1 # real 258m32.140s cat fb.criGriChoV1.chainCriGri1Link.txt # 2274544087 bases of 2318132242 (98.120%) in intersection time (doBlastzChainNet.pl -verbose=2 \ /hive/data/genomes/criGri1/bed/lastzCriGriChoV1.2017-04-19/DEF -debug \ -continue=download -swap -chainMinScore=1000 -chainLinearGap=loose \ -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \ -stop=download -noDbNameCheck -syntenicNet) > download.log 2>&1 time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` criGriChoV1 criGri1) \ > rbest.log 2>&1 & # real 83m10.946s ############################################################################# # lastz/chain/net swap human/hg38 (DONE - 2017-04-13 - Hiram) # original alignment cat fb.hg38.chainCriGriChoV1Link.txt # 973293331 bases of 3049335806 (31.918%) in intersection # and for the swap: mkdir /hive/data/genomes/criGriChoV1/bed/blastz.hg38.swap cd /hive/data/genomes/criGriChoV1/bed/blastz.hg38.swap time (doBlastzChainNet.pl -verbose=2 \ /hive/data/genomes/hg38/bed/lastzCriGriChoV1.2017-04-13/DEF \ -swap -chainMinScore=3000 -chainLinearGap=medium \ -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \ -noDbNameCheck -syntenicNet) > swap.log 2>&1 # real 91m19.847s cat fb.criGriChoV1.chainHg38Link.txt # 935724011 bases of 2318132242 (40.365%) in intersection time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` criGriChoV1 hg38) \ > rbest.log 2>&1 & # real 436m55.979s ############################################################################# # lastz/chain/net swap mouse/mm10 (DONE - 2017-04-13 - Hiram) # original alignment cat fb.mm10.chainCriGriChoV1Link.txt # 1553371182 bases of 2652783500 (58.556%) in intersection mkdir /hive/data/genomes/criGriChoV1/bed/blastz.mm10.swap cd /hive/data/genomes/criGriChoV1/bed/blastz.mm10.swap time (doBlastzChainNet.pl -verbose=2 \ /hive/data/genomes/mm10/bed/lastzCriGriChoV1.2017-04-13/DEF \ -noDbNameCheck -swap -syntenicNet \ -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \ -chainMinScore=3000 -chainLinearGap=medium) > swap.log 2>&1 & # real 157m21.977s cat fb.criGriChoV1.chainMm10Link.txt # 1513594461 bases of 2318132242 (65.294%) in intersection time (doRecipBest.pl -workhorse=hgwdev criGriChoV1 mm10 \ -buildDir=`pwd` -workhorse=hgwdev) > rbest.log 2>&1 & # real 769m8.998s ############################################################################## # Create kluster run files (DONE - 2017-04-13 - Hiram) # numerator is criGriChoV1 gapless bases "real" as reported by: featureBits -noRandom -noHap criGriChoV1 gap # 81654506 bases of 2318132242 (3.522%) 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 \( 2318132242 / 2861349177 \) \* 1024 # ( 2318132242 / 2861349177 ) * 1024 = 829.597253 # ==> use -repMatch=800 according to size scaled down from 1024 for human. # and rounded down to nearest 100 cd /hive/data/genomes/criGriChoV1 blat criGriChoV1.2bit \ /dev/null /dev/null -tileSize=11 -makeOoc=jkStuff/criGriChoV1.11.ooc \ -repMatch=800 # Wrote 24542 overused 11-mers to jkStuff/criGriChoV1.11.ooc # criGri1 was: # Wrote 21108 overused 11-mers to jkStuff/criGri1.11.ooc # check non-bridged gaps to see what the typical size is: # there are no non-bridged gaps in this assembly: hgsql -N -e 'select bridge from gap;' criGriChoV1 | sort | uniq -c # 156635 yes # if there are, scan their sizes: hgsql -N \ -e 'select * from gap where bridge="no" order by size;' criGriChoV1 \ | sort -k7,7nr | ave -col=7 stdin # and make a gap lift file for genbank # # all these gap sizes are 100 # # minimum gap size is 100 and produces a reasonable number of lifts # gapToLift -verbose=2 -minGap=10 criGriChoV1 jkStuff/nonBridged.lft \ # -bedFile=jkStuff/nonBridged.bed ######################################################################### # GENBANK AUTO UPDATE (DONE - 2017-04-13 - Hiram) ssh hgwdev cd $HOME/kent/src/hg/makeDb/genbank git pull # /cluster/data/genbank/data/organism.lst shows: # #organism mrnaCnt estCnt refSeqCnt # Cricetulus griseus 90138 12 345 # Organism name: Cricetulus griseus (Chinese hamster) # edit etc/genbank.conf to add criGriChoV1 just before criGri1 # criGriChoV1 (Cricetulus griseus - Chinese hamster ovary cell line CHO-K1) criGriChoV1.serverGenome = /hive/data/genomes/criGriChoV1/criGriChoV1.2bit criGriChoV1.clusterGenome = /hive/data/genomes/criGriChoV1/criGriChoV1.2bit criGriChoV1.ooc = /hive/data/genomes/criGriChoV1/jkStuff/criGriChoV1.11.ooc criGriChoV1.lift = no criGriChoV1.downloadDir = criGriChoV1 criGriChoV1.perChromTables = no criGriChoV1.refseq.mrna.native.pslCDnaFilter = ${lowCover.refseq.mrna.native.pslCDnaFilter} criGriChoV1.refseq.mrna.xeno.pslCDnaFilter = ${lowCover.refseq.mrna.xeno.pslCDnaFilter} criGriChoV1.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter} criGriChoV1.genbank.mrna.xeno.pslCDnaFilter = ${lowCover.genbank.mrna.xeno.pslCDnaFilter} criGriChoV1.genbank.est.native.pslCDnaFilter = ${lowCover.genbank.est.native.pslCDnaFilter} # DO NOT NEED genbank.mrna.xeno except for human, mouse # defaults yes: genbank.mrna.native.load, genbank.mrna.native.loadDesc, # genbank.est.native.load, refseq.mrna.native.load, refseq.mrna.native.loadDesc, # refseq.mrna.xeno.load , refseq.mrna.xeno.loadDesc # criGriChoV1.upstreamGeneTbl = ensGene # criGriChoV1.upstreamMaf = multiz9way /hive/data/genomes/criGriChoV1/bed/multiz9way/species.list git commit -m 'adding criGriChoV1 Cricetulus griseus - Chinese hamster ovary cell line CHO-K1 refs #19228' etc/genbank.conf git push # update /cluster/data/genbank/: make etc-update cd /cluster/data/genbank time ./bin/gbAlignStep -initial criGriChoV1 # logFile: var/build/logs/2017.04.13-10:50:30.criGriChoV1.initalign.log # real 1744m57.359s tail -2 var/build/logs/2017.04.13-10:50:30.criGriChoV1.initalign.log # hgwdev 2017.04.14-15:54:57 criGriChoV1.initalign: Succeeded: criGriChoV1 # hgwdev 2017.04.14-15:55:28 criGriChoV1.initalign: finish # To re-do, rm the dir first: # /cluster/data/genbank/work/initial.criGriChoV1 # load database when finished ssh hgwdev cd /cluster/data/genbank time ./bin/gbDbLoadStep -drop -initialLoad criGriChoV1 # logFile: var/dbload/hgwdev/logs/2017.04.19-10:31:05.criGriChoV1.dbload.log # real 30m42.283s tail -1 var/dbload/hgwdev/logs/2017.04.19-10:31:05.criGriChoV1.dbload.log # hgwdev 2017.04.19-10:49:44 criGriChoV1.dbload: finish # enable daily alignment and update of hgwdev cd ~/kent/src/hg/makeDb/genbank git pull # add criGriChoV1 to: # etc/align.dbs etc/hgwdev.dbs git add etc/align.dbs etc/hgwdev.dbs git commit -m 'adding criGriChoV1 to the update alignments refs #19228' etc/align.dbs etc/hgwdev.dbs git push make etc-update ############################################################################# # ncbiRefSeq (TBD - 2016-05-13 - Hiram) mkdir /hive/data/genomes/criGriChoV1/bed/ncbiRefSeq cd /hive/data/genomes/criGriChoV1/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 criGriChoV1) > 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 criGriChoV1) > 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 criGriChoV1) > load.log 2>&1 # real 0m33.205s cat fb.ncbiRefSeq.criGriChoV1.txt # 82563006 bases of 1218501075 (6.776%) in intersection featureBits -enrichment criGriChoV1 refGene ncbiRefSeq # refGene 1.181%, ncbiRefSeq 6.776%, both 1.175%, cover 99.49%, # enrich 14.68x ######################################################################### # BLATSERVERS ENTRY (DONE - 2017-04-19 - 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 ("criGriChoV1", "blat1a", "17872", "1", "0"); \ INSERT INTO blatServers (db, host, port, isTrans, canPcr) \ VALUES ("criGriChoV1", "blat1a", "17873", "0", "1");' \ hgcentraltest # test it with some sequence ############################################################################ ## set default position upon recommendation from Regeneron ## (DONE - 2017-05-12 - Hiram) ssh hgwdev hgsql -e 'update dbDb set defaultPos="NW_003613923v1:714339-726966" where name="criGriChoV1";' hgcentraltest ######################################################################### # all.joiner update, downloads and in pushQ - (DONE - 2017-04-25 - Hiram) cd $HOME/kent/src/hg/makeDb/schema # fixup all.joiner until this is a clean output joinerCheck -database=criGriChoV1 -tableCoverage all.joiner joinerCheck -database=criGriChoV1 -times all.joiner joinerCheck -database=criGriChoV1 -keys all.joiner cd /hive/data/genomes/criGriChoV1 time (makeDownloads.pl -workhorse=hgwdev criGriChoV1) > downloads.log 2>&1 # real 22m35.669s # now ready for pushQ entry mkdir /hive/data/genomes/criGriChoV1/pushQ cd /hive/data/genomes/criGriChoV1/pushQ time (makePushQSql.pl -redmineList criGriChoV1) \ > criGriChoV1.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/criGriChoV1/wib/gc5Base.wib # WARNING: hgwdev does not have /gbdb/criGriChoV1/wib/quality.wib # WARNING: hgwdev does not have /gbdb/criGriChoV1/bbi/quality.bw # WARNING: criGriChoV1 does not have seq # WARNING: criGriChoV1 does not have extFile # enter the path names to the redmine listings in the redmine issue # refs 19228 ######################################################################### # LIFTOVER TO criGriChoV2 (DONE - 2018-01-05 - Hiram) ssh hgwdev mkdir /hive/data/genomes/criGriChoV1/bed/blat.criGriChoV2.2018-01-05 cd /hive/data/genomes/criGriChoV1/bed/blat.criGriChoV2.2018-01-05 time (doSameSpeciesLiftOver.pl -verbose=2 -buildDir=`pwd` \ -ooc=/hive/data/genomes/criGriChoV1/jkStuff/criGriChoV1.11.ooc \ -bigClusterHub=ku -dbHost=hgwdev -workhorse=hgwdev \ criGriChoV1 criGriChoV2) > do.log 2>&1 # real 1030m38.867s # verify the convert link on the test browser is now active from # from criGriChoV1 to criGriChoV2 #########################################################################