# for emacs: -*- mode: sh; -*- # This file describes browser build for the casCan1 ######################################################################### # photograph obtained # (DONE - 2018-03-16 - Hiram) mkdir -p /hive/data/genomes/casCan1/photo cd /hive/data/genomes/casCan1/photo wget --timestamping \ "https://farm3.staticflickr.com/2537/4154614438_685a78fac5_o_d.jpg" convert -quality 100 -crop 1920x2160+240+640 \ 4154614438_685a78fac5_o_d.jpg crop.jpg convert -quality 80 -geometry 400x400 crop.jpg Castor_canadensis.jpg cd /hive/data/genomes/casCan1 printf 'photoCreditURL\thttps://www.flickr.com/photos/colink/4154614438/in/photostream/ photoCreditName\tColin Knowles, flickr ' > photoReference.txt cat photoReference.txt photoCreditURL https://www.flickr.com/photos/colink/4154614438/in/photostream/ photoCreditName Colin Knowles, flickr ######################################################################### # Initial steps (DONE - 2018-03-16 - Hiram) # To start this initialBuild.txt document, from a previous assembly document: mkdir ~/kent/src/hg/makeDb/doc/casCan1 cd ~/kent/src/hg/makeDb/doc/casCan1 # best to use a most recent document with similar assembly structure # since it has the latest features and procedures: sed -e 's/thaSir1/casCan1/g; s/ThaSir1/CasCan1/g; s/DONE/TBD/g;' \ ../thaSir1/initialBuild.txt > initialBuild.txt mkdir /hive/data/genomes/casCan1/refseq cd /hive/data/genomes/casCan1/refseq rsync -L -a -P \ rsync://ftp.ncbi.nlm.nih.gov/genomes/refseq/vertebrate_mammalian/Castor_canadensis/all_assembly_versions/GCF_001984765.1_C.can_genome_v1.0/ ./ # sent 527 bytes received 2920862995 bytes 21716457.41 bytes/sec # total size is 2920503870 speedup is 1.00 # real 2m13.873s # check assembly size for later reference: faSize G*0_genomic.fna.gz # 2518306565 bases (331911 N's 2517974654 real 1726468223 upper # 791506431 lower) in 21157 sequences in 1 files # Total size: mean 119029.5 sd 206582.1 min 202 (NW_017887296.1) # max 4235486 (NW_017869957.1) median 42406 # %31.43 masked total, %31.43 masked real # this information is from the top of # casCan1/refseq/GCF_001984765.1_C.can_genome_v1.0_assembly_report.txt # Assembly name: C.can genome v1.0 # Organism name: Castor canadensis (American beaver) # Isolate: Ward # Sex: male # Taxid: 51338 # BioSample: SAMN06187566 # BioProject: PRJNA359140 # Submitter: Hospital for Sick Children # Date: 2017-2-4 # Assembly type: haploid # Release type: major # Assembly level: Scaffold # Genome representation: full # WGS project: MTKA01 # Assembly method: ABySS v. 1.9.0; Canu v. 1.2; Platanus v. 1.2.4 # Expected final version: no # Reference guided assembly: de-novo # Genome coverage: 110.0x # Sequencing technology: Illumina HiSeq; PacBio # RefSeq category: Representative Genome # GenBank assembly accession: GCA_001984765.1 # RefSeq assembly accession: GCF_001984765.1 # RefSeq assembly and GenBank assemblies identical: yes # ## Assembly-Units: ## GenBank Unit Accession RefSeq Unit Accession Assembly-Unit name ## GCA_001984775.1 GCF_001984775.1 Primary Assembly ############################################################################# # establish config.ra file (DONE - Hiram - 2018-03-16) # arguments here are: cd /hive/data/genomes/casCan1 $HOME/kent/src/hg/utils/automation/prepConfig.pl casCan1 mammal \ mammal ./refseq/*_assembly_report.txt > casCan1.config.ra # going to need a mitoAcc ? # fixup commonName to: commonName Beaver # set mitoAcc to none, the refseq assembly did not have one # reset orderKey to be correct for "Beaver": 2200 # verify it looks sane cat casCan1.config.ra # config parameters for makeGenomeDb.pl: db casCan1 clade mammal genomeCladePriority 35 scientificName Castor canadensis commonName Beaver assemblyDate Feb. 2017 assemblyLabel Hospital for Sick Children assemblyShortLabel C.can genome v1.0 orderKey 2200 mitoAcc none fastaFiles /hive/data/genomes/casCan1/ucsc/*.fa.gz agpFiles /hive/data/genomes/casCan1/ucsc/*.agp # qualFiles none dbDbSpeciesDir mammal photoCreditURL https://www.flickr.com/photos/colink/4154614438/in/photostream/ photoCreditName Colin Knowles, flickr ncbiGenomeId 9723 ncbiAssemblyId 994011 ncbiAssemblyName C.can genome v1.0 ncbiBioProject 359140 ncbiBioSample SAMN06187566 genBankAccessionID GCF_001984765.1 taxId 51338 ############################################################################# # setup UCSC named files (DONE - 2018-03-16 - Hiram) mkdir /hive/data/genomes/casCan1/ucsc cd /hive/data/genomes/casCan1/ucsc # check for duplicate sequences: time faToTwoBit -noMask ../refseq/G*0_genomic.fna.gz refseq.2bit # real 1m1.756s twoBitDup refseq.2bit # no output is a good result, otherwise, would have to eliminate duplicates # there is no assembly structure directory in this refseq release # simply need to fix the contig names from .1 to v1 time zcat ../refseq/GCF_001984765.1_C.can_genome_v1.0_assembly_structure/Primary_Assembly/unplaced_scaffolds/FASTA//unplaced.scaf.fna.gz \ | sed -e 's/.1 Castor.*/v1/;' | gzip -c > chrUn.fa.gz # real 6m9.522s # survey the gap structure: twoBitInfo -nBed refseq.2bit stdout | gzip -c > refseq.N.bed.gz time zcat ../refseq/GCF_001984765.1_C.can_genome_v1.0_assembly_structure/Primary_Assembly/unplaced_scaffolds/AGP//unplaced.scaf.agp.gz \ | sed -e 's/.1\t/v1\t/;' > chrUn.agp # the AGP does not mark any of the N's: awk '$5 == "N"' chrUn.agp # no output, no gaps in the AGP file # awk '$5 == "N"' chrUn.agp | ave -col=6 stdin | grep -w total # there are 331,911 bases in gap: zcat refseq.N.bed.gz | awk '{print $3-$2}' | ave stdin | grep -w total # total 331911.000000 # construct a fake AGP to get the gaps annotated mv chrUn.agp chrUn.agp.noGaps hgFakeAgp -minContigGap=1 chrUn.fa.gz chrUn.fake.agp awk '$5 == "N"' chrUn.fake.agp | ave -col=6 stdin Q1 100.000000 median 100.000000 Q3 100.000000 average 99.943089 min 1.000000 max 100.000000 count 3321 total 331911.000000 standard deviation 2.321342 # verify fasta and AGPs agree time faToTwoBit chrUn.fa.gz test.2bit # real 1m11.028s time checkAgpAndFa chrUn.fake.agp test.2bit 2>&1 | tail -4 # All AGP and FASTA entries agree - both files are valid # real 0m31.258s # and no sequence lost from original: twoBitToFa test.2bit stdout | faSize stdin # 2518306565 bases (331911 N's 2517974654 real 2517974654 upper 0 lower) # in 21157 sequences in 1 files # Total size: mean 119029.5 sd 206582.1 min 202 (NW_017887296v1) # max 4235486 (NW_017869957v1) median 42406 # original: # 2518306565 bases (331911 N's 2517974654 real 1726468223 upper # 791506431 lower) in 21157 sequences in 1 files # no longer need these temporary 2bit files rm refseq.2bit test.2bit refseq.N.bed.gz # run up idKeys for later use for ucscToRefSeq and chromAlias mkdir /hive/data/genomes/casCan1/refseq/idKeys cd /hive/data/genomes/casCan1/refseq/idKeys faToTwoBit ../G*.0_genomic.fna.gz refseq.casCan1.2bit time (doIdKeys.pl -buildDir=`pwd` -twoBit=`pwd`/refseq.casCan1.2bit \ refseqCasCan1) > do.log 2>&1 # real 15m13.836s cat refseqCasCan1.keySignature.txt # aabc4f017046517667db0eb1192e34e2 ############################################################################# # Initial database build (DONE - 2018-03-16 - Hiram) cd /hive/data/genomes/casCan1 # verify sequence and AGP are OK: time (makeGenomeDb.pl -workhorse=hgwdev -dbHost=hgwdev -fileServer=hgwdev \ -stop=agp casCan1.config.ra) > agp.log 2>&1 # *** All done! (through the 'agp' step) # real 3m5.714s # then finish it off: time (makeGenomeDb.pl -workhorse=hgwdev -dbHost=hgwdev \ -fileServer=hgwdev -continue=db casCan1.config.ra) > db.log 2>&1 # real 22m54.296s # check in the trackDb files created in TemporaryTrackDbCheckout/ # and add casCan1 to trackDb/makefile # temporary symlink until masked sequence is available cd /hive/data/genomes/casCan1 ln -s `pwd`/casCan1.unmasked.2bit /gbdb/casCan1/casCan1.2bit ############################################################################## # cpgIslands on UNMASKED sequence (DONE - 2018-03-16 - Hiram) mkdir /hive/data/genomes/casCan1/bed/cpgIslandsUnmasked cd /hive/data/genomes/casCan1/bed/cpgIslandsUnmasked time (doCpgIslands.pl -dbHost=hgwdev -bigClusterHub=ku -buildDir=`pwd` \ -tableName=cpgIslandExtUnmasked \ -maskedSeq=/hive/data/genomes/casCan1/casCan1.unmasked.2bit \ -workhorse=hgwdev -smallClusterHub=ku casCan1) > do.log 2>&1 # real 5m14.124s cat fb.casCan1.cpgIslandExtUnmasked.txt # 18068964 bases of 2517974654 (0.718%) in intersection ############################################################################# # cytoBandIdeo - (DONE - 2018-03-16 - Hiram) mkdir /hive/data/genomes/casCan1/bed/cytoBand cd /hive/data/genomes/casCan1/bed/cytoBand makeCytoBandIdeo.csh casCan1 ########################################################################## # run up idKeys files for chromAlias (DONE - 2018-03-16 - Hiram) mkdir /hive/data/genomes/casCan1/bed/idKeys cd /hive/data/genomes/casCan1/bed/idKeys time (doIdKeys.pl -twoBit=/hive/data/genomes/casCan1/casCan1.unmasked.2bit -buildDir=`pwd` casCan1) > do.log 2>&1 & # real 14m47.063s cat casCan1.keySignature.txt # aabc4f017046517667db0eb1192e34e2 ########################################################################## # run up gapOverlap track (DONE - 2018-03-16 - Hiram) mkdir /hive/data/genomes/casCan1/bed/gapOverlap cd /hive/data/genomes/casCan1/bed/gapOverlap time (doGapOverlap.pl casCan1 \ -twoBit="/hive/data/genomes/casCan1/casCan1.unmasked.2bit" \ -buildDir=`pwd`) > do.log 2>&1 # real 1m53.463s cat fb.casCan1.gapOverlap.txt # 4928 bases of 2518306565 (0.000%) in intersection bigBedInfo casCan1.gapOverlap.bb version: 4 fieldCount: 12 hasHeaderExtension: yes isCompressed: yes isSwapped: 0 extraIndexCount: 0 itemCount: 19 primaryDataSize: 1,364 primaryIndexSize: 6,348 zoomLevels: 3 chromCount: 19 basesCovered: 6,828 ########################################################################## # run up tandemDups track (DONE - 2018-03-17 - Hiram) mkdir /hive/data/genomes/casCan1/bed/tandemDups cd /hive/data/genomes/casCan1/bed/tandemDups time (~/kent/src/hg/utils/automation/doTandemDup.pl \ -twoBit="/hive/data/genomes/casCan1/casCan1.unmasked.2bit" \ casCan1) > do.log 2>&1 # real 58m42.975s cat fb.casCan1.tandemDups.txt # 30226302 bases of 2518306565 (1.200%) in intersection bigBedInfo casCan1.tandemDups.bb version: 4 fieldCount: 13 hasHeaderExtension: yes isCompressed: yes isSwapped: 0 extraIndexCount: 0 itemCount: 463,378 primaryDataSize: 11,472,847 primaryIndexSize: 431,732 zoomLevels: 6 chromCount: 13097 basesCovered: 431,491,745 meanDepth (of bases covered): 6.825069 minDepth: 1.000000 maxDepth: 2053.000000 std of depth: 19.209676 ########################################################################## # ucscToINSDC and ucscToRefSeq table/track (DONE - 2018-03-21 - 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 # need the idKeys for the genbank sequence: mkdir /hive/data/genomes/casCan1/genbank/idKeys faToTwoBit /hive/data/outside/ncbi/genomes/genbank/vertebrate_mammalian/Castor_canadensis/all_assembly_versions/GCA_001984765.1_C.can_genome_v1.0/GCA_001984765.1_C.can_genome_v1.0_genomic.fna.gz \ genbank.casCan1.2bit time (doIdKeys.pl -buildDir=`pwd` -twoBit=`pwd`/genbank.casCan1.2bit \ genbankCasCan1) > do.log 2>&1 # real 24m45.103s cat genbankCasCan1.keySignature.txt # aabc4f017046517667db0eb1192e34e2 mkdir /hive/data/genomes/casCan1/bed/ucscToINSDC cd /hive/data/genomes/casCan1/bed/ucscToINSDC join -t$'\t' ../idKeys/casCan1.idKeys.txt \ ../../genbank/idKeys/genbankCasCan1.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/casCan1.idKeys.txt \ ../../refseq/idKeys/refseqCasCan1.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, only one for the RefSeq: wc -l * ../../chrom.sizes # 21157 ucscToINSDC.bed # 21157 ucscToRefSeq.bed # 21157 ../../chrom.sizes export chrSize=`cut -f1 ucscToINSDC.bed | awk '{print length($0)}' | sort -n | tail -1` echo $chrSize # 14 # use the 14 in this sed sed -e "s/21/$chrSize/" $HOME/kent/src/hg/lib/ucscToINSDC.sql \ | hgLoadSqlTab casCan1 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/" $HOME/kent/src/hg/lib/ucscToINSDC.sql \ | sed -e 's/INSDC/RefSeq/g;' \ | hgLoadSqlTab casCan1 ucscToRefSeq stdin ucscToRefSeq.bed # checkTableCoords should be silent checkTableCoords casCan1 # each should cover %100 entirely: featureBits -countGaps casCan1 ucscToINSDC # 2518306565 bases of 2518306565 (100.000%) in intersection featureBits -countGaps casCan1 ucscToRefSeq # 2518306565 bases of 2518306565 (100.000%) in intersection ######################################################################### # add chromAlias table (DONE - 2018-03-21 - Hiram) mkdir /hive/data/genomes/casCan1/bed/chromAlias cd /hive/data/genomes/casCan1/bed/chromAlias hgsql -N -e 'select chrom,name from ucscToRefSeq;' casCan1 \ > ucsc.refseq.tab hgsql -N -e 'select chrom,name from ucscToINSDC;' casCan1 \ > ucsc.genbank.tab ~/kent/src/hg/utils/automation/chromAlias.pl ucsc.*.tab \ > casCan1.chromAlias.tab for t in refseq genbank do c0=`cat ucsc.$t.tab | wc -l` c1=`grep $t casCan1.chromAlias.tab | wc -l` ok="OK" if [ "$c0" -ne "$c1" ]; then ok="ERROR" fi printf "# checking $t: $c0 =? $c1 $ok\n" done # checking refseq: 21157 =? 21157 OK # checking genbank: 21157 =? 21157 OK hgLoadSqlTab casCan1 chromAlias ~/kent/src/hg/lib/chromAlias.sql \ casCan1.chromAlias.tab ######################################################################### # fixup search rule for assembly track/gold table (DONE - 2018-03-21 - Hiram) cd ~/kent/src/hg/makeDb/trackDb/mammal/casCan1 # preview prefixes and suffixes: hgsql -N -e "select frag from gold;" casCan1 \ | sed -e 's/[0-9][0-9]*//;' | sort | uniq -c # 21157 NW_v1_1 # 15 NW_v1_10 # ... etc ... # 1 NW_v1_33 # 372 NW_v1_4 # 219 NW_v1_5 # 126 NW_v1_6 # 75 NW_v1_7 # 51 NW_v1_8 # 28 NW_v1_9 # implies a rule: 'NW_0178[0-9]{4}[0-9]*(v1_[0-9]+)?' # verify this rule will find them all and eliminate them all: hgsql -N -e "select frag from gold;" casCan1 | wc -l # 24478 hgsql -N -e "select frag from gold;" casCan1 \ | egrep -e 'NW_0178[0-9]{4}[0-9]*(v1_[0-9]+)?' | wc -l # 24478 hgsql -N -e "select frag from gold;" casCan1 \ | egrep -v -e 'NW_0178[0-9]{4}[0-9]*(v1_[0-9]+)?' | wc -l # 0 # hence, add to trackDb/reptile/casCan1/trackDb.ra searchTable gold shortCircuit 1 termRegex NW_0178[0-9]{4}[0-9]*(v1_[0-9]+)? query select chrom,chromStart,chromEnd,frag from %s where frag like '%s%%' searchPriority 8 # verify searches work in the position box for these name patterns ########################################################################## # running repeat masker (DONE - 2018-03-17 - Hiram) mkdir /hive/data/genomes/casCan1/bed/repeatMasker cd /hive/data/genomes/casCan1/bed/repeatMasker # trying new version of RM time (~/kent/src/hg/utils/automation/doRepeatMasker.pl -buildDir=`pwd` \ -bigClusterHub=ku -dbHost=hgwdev -workhorse=hgwdev \ -smallClusterHub=ku casCan1) > do.log 2>&1 & # real 100m48.992s # one broken item: # RepeatMasker bug?: Undefined id, line 1145096 of input: # 384 30.1 7.1 6.3 NW_017870925v1 247145 247272 (1754782) + MLT1D-int # LTR/ERVL-MaLR 1233 1355 (16) mv casCan1.fa.out casCan1.fa.out.broken mv casCan1.sorted.fa.out casCan1.sorted.fa.out.broken grep -v "NW_017870925v1 247145 247272" casCan1.sorted.fa.out.broken \ > casCan1.sorted.fa.out grep -v "NW_017870925v1 247145 247272" casCan1.fa.out.broken \ > casCan1.fa.out /cluster/home/hiram/kent/src/hg/utils/automation/extractNestedRepeats.pl \ casCan1.fa.out | sort -k1,1 -k2,2n > casCan1.nestedRepeats.bed time (~/kent/src/hg/utils/automation/doRepeatMasker.pl -buildDir=`pwd` \ -bigClusterHub=ku -dbHost=hgwdev -workhorse=hgwdev \ -continue=mask -smallClusterHub=ku casCan1) > mask.log 2>&1 & # real 22m0.703s egrep "bases|Total|masked" faSize.rmsk.txt \ | fold -w 75 -s | sed -e 's/^/# /;' # 2518306565 bases (331911 N's 2517974654 real 1691459912 upper 826514742 # lower) in 21157 sequences in 1 files # Total size: mean 119029.5 sd 206582.1 min 202 (NW_017887296v1) max 4235486 # (NW_017869957v1) median 42406 # %32.82 masked total, %32.82 masked real egrep -i "versi|relea" do.log # February 01 2017 (open-4-0-7) 1.331 version of RepeatMasker # CC Dfam_Consensus RELEASE 20170127; * # CC RepBase RELEASE 20170127; time featureBits -countGaps casCan1 rmsk # 826515301 bases of 2518306565 (32.820%) in intersection # real 0m39.362s # 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;' casCan1 \ | bedSingleCover.pl stdin | ave -col=4 stdin | grep "^total" # total 826515301.000000 # real 0m32.096s ########################################################################## # running simple repeat (DONE - 2018-03-17 - Hiram) mkdir /hive/data/genomes/casCan1/bed/simpleRepeat cd /hive/data/genomes/casCan1/bed/simpleRepeat # using trf409 5 here a bit smaller genome (human == 6) time (doSimpleRepeat.pl -buildDir=`pwd` -bigClusterHub=ku \ -dbHost=hgwdev -workhorse=hgwdev -smallClusterHub=ku \ -trf409 5 casCan1) > do.log 2>&1 & # real 12m8.981s cat fb.simpleRepeat # 32754592 bases of 2517974654 (1.301%) in intersection # adding this trfMask to the other masking cd /hive/data/genomes/casCan1 # when using the Window Masker result: # twoBitMask bed/windowMasker/casCan1.cleanWMSdust.2bit \ # -add bed/simpleRepeat/trfMask.bed casCan1.2bit # you can safely ignore the warning about fields >= 13 # when using Rmsk results, add to rmsk after it is done: twoBitMask casCan1.rmsk.2bit \ -add bed/simpleRepeat/trfMask.bed casCan1.2bit # you can safely ignore the warning about fields >= 13 twoBitToFa casCan1.2bit stdout | faSize stdin > faSize.casCan1.2bit.txt egrep "bases|Total|masked" faSize.casCan1.2bit.txt \ | fold -w 78 -s | sed -e 's/^/# /;' # 2518306565 bases (331911 N's 2517974654 real 1690683148 upper 827291506 # lower) in 21157 sequences in 1 files # Total size: mean 119029.5 sd 206582.1 min 202 (NW_017887296v1) max 4235486 # (NW_017869957v1) median 42406 # %32.85 masked total, %32.86 masked real # reset the symlink rm /gbdb/casCan1/casCan1.2bit ln -s `pwd`/casCan1.2bit /gbdb/casCan1/casCan1.2bit ######################################################################### # CREATE MICROSAT TRACK (DONE - 2018-03-17 - Hiram) ssh hgwdev mkdir /cluster/data/casCan1/bed/microsat cd /cluster/data/casCan1/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 casCan1 microsat microsat.bed # Read 42247 elements of size 4 from microsat.bed ########################################################################## ## WINDOWMASKER (DONE - 2018-03-17 - Hiram) mkdir /hive/data/genomes/casCan1/bed/windowMasker cd /hive/data/genomes/casCan1/bed/windowMasker time (doWindowMasker.pl -buildDir=`pwd` -workhorse=hgwdev \ -dbHost=hgwdev casCan1) > do.log 2>&1 # real 154m29.883s # Masking statistics egrep "bases|Total|masked" faSize.casCan1.cleanWMSdust.txt \ | fold -w 78 -s | sed -e 's/^/# /;' # 2518306565 bases (331911 N's 2517974654 real 1713155625 upper 804819029 # lower) in 21157 sequences in 1 files # Total size: mean 119029.5 sd 206582.1 min 202 (NW_017887296v1) max 4235486 # (NW_017869957v1) median 42406 # %31.96 masked total, %31.96 masked real cat fb.casCan1.rmsk.windowmaskerSdust.txt # 402462670 bases of 2518306565 (15.981%) in intersection ########################################################################## # cpgIslands - (DONE - 2018-03-19 - Hiram) mkdir /hive/data/genomes/casCan1/bed/cpgIslands cd /hive/data/genomes/casCan1/bed/cpgIslands time (doCpgIslands.pl -dbHost=hgwdev -bigClusterHub=ku \ -workhorse=hgwdev -smallClusterHub=ku casCan1) > do.log 2>&1 & # real 5m34.044s cat fb.casCan1.cpgIslandExt.txt # 16800578 bases of 2517974654 (0.667%) in intersection ############################################################################## # genscan - (DONE - 2018-03-17 - Hiram) mkdir /hive/data/genomes/casCan1/bed/genscan cd /hive/data/genomes/casCan1/bed/genscan time (doGenscan.pl -buildDir=`pwd` -workhorse=hgwdev -dbHost=hgwdev \ -bigClusterHub=ku casCan1) > do.log 2>&1 & # real 32m23.411s cat fb.casCan1.genscan.txt # 59378168 bases of 2517974654 (2.358%) in intersection cat fb.casCan1.genscanSubopt.txt # 66045114 bases of 2517974654 (2.623%) in intersection ############################################################################# # augustus gene track (DONE - 2018-03-17 - Hiram) mkdir /hive/data/genomes/casCan1/bed/augustus cd /hive/data/genomes/casCan1/bed/augustus time (doAugustus.pl -buildDir=`pwd` -bigClusterHub=ku \ -species=human -dbHost=hgwdev -workhorse=hgwdev casCan1) \ > do.log 2>&1 & # real 55m59.141s cat fb.casCan1.augustusGene.txt # 52082785 bases of 2517974654 (2.068%) in intersection ############################################################################## # lastz/chain/net swap human/hg38 (DONE - 2018-03-19 - Hiram) # alignment on hg38 cd /hive/data/genomes/hg38/bed/lastzCasCan1.2018-02-19 cat fb.hg38.chainCasCan1Link.txt # 1440538496 bases of 3049335806 (47.241%) in intersection cat fb.hg38.chainSynCasCan1Link.txt # 1348638697 bases of 3049335806 (44.227%) in intersection cat fb.hg38.chainRBestCasCan1Link.txt # 1318039475 bases of 3049335806 (43.224%) in intersection # and for the swap: mkdir /hive/data/genomes/casCan1/bed/blastz.hg38.swap cd /hive/data/genomes/casCan1/bed/blastz.hg38.swap time (doBlastzChainNet.pl -verbose=2 \ /hive/data/genomes/hg38/bed/lastzCasCan1.2018-03-19/DEF \ -chainMinScore=3000 -chainLinearGap=medium \ -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \ -swap -syntenicNet) > swap.log 2>&1 & # real 141m44.555s cat fb.casCan1.chainHg38Link.txt # 1440839903 bases of 2517974654 (57.222%) in intersection cat fb.casCan1.chainSynHg38Link.txt # 1348477433 bases of 2517974654 (53.554%) in intersection time (doRecipBest.pl -load -workhorse=hgwdev \ -buildDir=`pwd` casCan1 hg38) > rbest.log 2>&1 & # real 1199m30.336s cat fb.casCan1.chainRBestHg38Link.txt # 1321240715 bases of 2517974654 (52.472%) in intersection ############################################################################## # lastz/chain/net swap mouse/mm10 (DONE - 2018-03-19 - Hiram) # original alignment to mm10 cd /hive/data/genomes/mm10/bed/lastzCasCan1.2018-03-19 cat fb.mm10.chainCasCan1Link.txt # 969752969 bases of 2652783500 (36.556%) in intersection cat fb.mm10.chainRBestCasCan1Link.txt # 912108399 bases of 2652783500 (34.383%) in intersection mkdir /hive/data/genomes/casCan1/bed/blastz.mm10.swap cd /hive/data/genomes/casCan1/bed/blastz.mm10.swap time (doBlastzChainNet.pl -verbose=2 \ /hive/data/genomes/mm10/bed/lastzCasCan1.2018-03-19/DEF \ -swap -syntenicNet \ -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \ -chainMinScore=3000 -chainLinearGap=medium) > swap.log 2>&1 # real 100m12.450s cat fb.casCan1.chainMm10Link.txt # 1027587643 bases of 2517974654 (40.810%) in intersection cat fb.casCan1.chainSynMm10Link.txt # 876969229 bases of 2517974654 (34.828%) in intersection time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` casCan1 mm10) \ > rbest.log 2>&1 # real 1280m7.127s cat fb.casCan1.chainRBestMm10Link.txt # 911437520 bases of 2517974654 (36.197%) in intersection ############################################################################## # Create kluster run files (DONE - 2018-03-17 - Hiram) # numerator is casCan1 gapless bases "real" as reported by: featureBits -noRandom -noHap casCan1 gap # 331911 bases of 2517974654 (0.013%) 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 \( 2517974654 / 2861349177 \) \* 1024 # ( 2517974654 / 2861349177 ) * 1024 = 901.115483 # ==> use -repMatch=900 according to size scaled down from 1024 for human. # and rounded to nearest 50 cd /hive/data/genomes/casCan1 blat casCan1.2bit \ /dev/null /dev/null -tileSize=11 -makeOoc=jkStuff/casCan1.11.ooc \ -repMatch=900 # Wrote 30908 overused 11-mers to jkStuff/casCan1.11.ooc # check non-bridged gaps to see what the typical size is: # there are no non-bridged gaps in this contig assembly hgsql -N \ -e 'select * from gap where bridge="no" order by size;' casCan1 \ | sort -k7,7nr | ave -col=7 stdin # Q1 127644.000000 # median 231535.000000 # Q3 500000.000000 # average 280957.457875 # min 50429.000000 # max 500000.000000 # count 273 # minimum non-bridged gap is 50000 # gapToLift -verbose=2 -minGap=50000 casCan1 jkStuff/nonBridged.lft \ # -bedFile=jkStuff/nonBridged.bed ######################################################################### # GENBANK AUTO UPDATE (DONE - 2018-01-19 - Hiram) ssh hgwdev cd $HOME/kent/src/hg/makeDb/genbank git pull # /cluster/data/genbank/data/organism.lst shows: # #organism mrnaCnt estCnt refSeqCnt # Castor canadensis 2 0 0 # edit src/lib/gbGenome.c to add thaSirNames definitions # static char *casCanNames[] = {"Castor canadensis", NULL}; # . . . # {"casCan", casCanNames}, # edit etc/genbank.conf to add casCan1 just before dipOrd1 # casCan1 (American beaver/Castor canadensis/taxId 51338) casCan1.serverGenome = /hive/data/genomes/casCan1/casCan1.2bit casCan1.clusterGenome = /hive/data/genomes/casCan1/casCan1.2bit casCan1.ooc = /hive/data/genomes/casCan1/jkStuff/casCan1.11.ooc casCan1.lift = no casCan1.refseq.mrna.native.pslCDnaFilter = ${ordered.refseq.mrna.native.pslCDnaFilter} casCan1.refseq.mrna.xeno.pslCDnaFilter = ${ordered.refseq.mrna.xeno.pslCDnaFilter} casCan1.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter} casCan1.genbank.mrna.xeno.pslCDnaFilter = ${ordered.genbank.mrna.xeno.pslCDnaFilter} casCan1.genbank.est.native.pslCDnaFilter = ${ordered.genbank.est.native.pslCDnaFilter} casCan1.genbank.est.xeno.pslCDnaFilter = ${ordered.genbank.est.xeno.pslCDnaFilter} # DO NOT NEED genbank.mrna.xeno except for human, mouse # defaults yes: genbank.mrna.native.load genbank.mrna.native.loadDesc # yes: genbank.est.native.load refseq.mrna.native.load # yes: refseq.mrna.native.loadDesc refseq.mrna.xeno.load # yes: refseq.mrna.xeno.loadDesc # defaults no: genbank.mrna.xeno.load genbank.mrna.xeno.loadDesc # no: genbank.est.native.loadDesc genbank.est.xeno.load # no: genbank.est.xeno.loadDesc # there are zero native est or refSeq for casCan1 casCan1.genbank.est.native.load = no casCan1.refseq.mrna.native.load = no casCan1.refseq.mrna.native.loadDesc = no casCan1.downloadDir = casCan1 casCan1.perChromTables = no # enable daily alignment and update of hgwdev # add casCan1 to: # etc/align.dbs etc/hgwdev.dbs git commit -m \ "Added casCan1/Castor canadensis/American beaver; refs #21116" \ src/lib/gbGenome.c etc/genbank.conf etc/align.dbs etc/hgwdev.dbs git push # update /cluster/data/genbank/: make install-server make etc-update # wait a couple days, the automatic daily runs of genbank will pick # this up and get the initial run done ############################################################################# # ncbiRefSeq (DONE - 2018-03-19 - Hiram) # when assembly is from refseq, can run up this track, not so genbank mkdir /hive/data/genomes/casCan1/bed/ncbiRefSeq cd /hive/data/genomes/casCan1/bed/ncbiRefSeq time (~/kent/src/hg/utils/automation/doNcbiRefSeq.pl -buildDir=`pwd` \ -bigClusterHub=ku -dbHost=hgwdev \ -fileServer=hgwdev -smallClusterHub=ku -workhorse=hgwdev \ refseq vertebrate_mammalian Castor_canadensis \ GCF_001984765.1_C.can_genome_v1.0 casCan1) > do.log 2>&1 # real 24m26.335s cat fb.ncbiRefSeq.casCan1.txt # 54122633 bases of 2517974654 (2.149%) in intersection # interesting to intersect with refGene track featureBits casCan1 -enrichment ncbiRefSeq refGene ############################################################################# # BLATSERVERS ENTRY (DONE - 2018-03-21 - 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 ("casCan1", "blat1d", "17896", "1", "0"); \ INSERT INTO blatServers (db, host, port, isTrans, canPcr) \ VALUES ("casCan1", "blat1d", "17897", "0", "1");' \ hgcentraltest # test it with some sequence ############################################################################ ## reset default position to DSPP gene location (DONE - 2018-03-21 - Hiram) ## where the beaver mRNA KY286067 ## is located. This is the gene for dentin sialophosphoprotein ## https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Search&db=PubMed&term=Dspp&doptcmdl=DocSum ssh hgwdev hgsql -e 'update dbDb set defaultPos="NW_017884132v1:4754-15103" where name="casCan1";' hgcentraltest ######################################################################### # all.joiner update, downloads and in pushQ - (DONE - 2018-03-21 - Hiram) cd $HOME/kent/src/hg/makeDb/schema ~/kent/src/hg/utils/automation/verifyBrowser.pl casCan1 # 59 tables in database casCan1 - Beaver, Castor canadensis # verified 58 tables, 1 extra tables, 9 optional tables # NCBI RefSeq genes 9 optional tables # 1 tantan - extra table # 6 genbank tables found # verified 43 tables, 0 missing tables # fixup all.joiner until this is a clean output joinerCheck -database=casCan1 -tableCoverage all.joiner joinerCheck -database=casCan1 -times all.joiner time joinerCheck -database=casCan1 -keys all.joiner # real 5m48.632s cd /hive/data/genomes/casCan1 time (makeDownloads.pl -workhorse=hgwdev casCan1) > downloads.log 2>&1 # real 46m7.888s # now ready for pushQ entry mkdir /hive/data/genomes/casCan1/pushQ cd /hive/data/genomes/casCan1/pushQ time (makePushQSql.pl -redmineList casCan1) > casCan1.pushQ.sql 2> stderr.out # real 7m9.557s # remove the tandemDups and gapOverlap from the listings: sed -i -e "/tandemDups/d" redmine.casCan1.table.list sed -i -e "/Tandem Dups/d" redmine.casCan1.releaseLog.txt sed -i -e "/gapOverlap/d" redmine.casCan1.table.list sed -i -e "/Gap Overlaps/d" redmine.casCan1.releaseLog.txt # check for errors in stderr.out, some are OK, e.g.: # WARNING: casCan1 does not have seq # WARNING: casCan1 does not have extFile ## there are warnings about the RBest and Syn chainNet tables, which we ## are not interested in at this time. They can be left out. # verify the file listings are valid, should be no output to stderr: cat redmine.casCan1.file.list \ | while read L; do ls -ogL $L; done > /dev/null # to verify the database.table list is correct, should be the same # line count for these two commands: wc -l redmine.casCan1.table.list # 46 redmine.casCan1.table.list awk -F'.' '{ printf "hgsql -N -e \"show table status like '"'"'%s'"'"';\" %s\n", $2, $1 }' redmine.casCan1.table.list | while read L; do eval $L; done | wc -l # 46 # enter the path names to these files in the redmine issue to # make QA Ready: ls `pwd`/redmine* /hive/data/genomes/casCan1/pushQ/redmine.casCan1.file.list /hive/data/genomes/casCan1/pushQ/redmine.casCan1.releaseLog.txt /hive/data/genomes/casCan1/pushQ/redmine.casCan1.table.list #########################################################################