ec42546aa8efd2a5801969e60dd52bb7d9d5948d galt Sat Apr 10 01:33:17 2021 -0700 fixing small error diff --git src/hg/makeDb/doc/grcM38P6.txt src/hg/makeDb/doc/grcM38P6.txt index 0c8d548..dfa7a34 100644 --- src/hg/makeDb/doc/grcM38P6.txt +++ src/hg/makeDb/doc/grcM38P6.txt @@ -1,389 +1,389 @@ # for emacs: -*- mode: sh; -*- ############################################################################## # GRCm38 patch 6 build: build basic tracks on separate database for new # sequences only (relative to mm10). ############################################################################## ############################################################################## # download or rather ln -s the patch release files (DONE - 2020-02-27 - Angie) # Note: newer assemblies use refseq releases instead of genbank, but mm10 uses genbank # so continue with that when building patches. mkdir -p /hive/data/genomes/grcM38P6/genbank cd /hive/data/genomes/grcM38P6/genbank # Releases have already been downloaded to /hive/data/outside/ncbi/genomes/. ln -s /hive/data/outside/ncbi/genomes/genbank/vertebrate_mammalian/Mus_musculus/all_assembly_versions/GCA_000001635.8_GRCm38.p6/* . ############################################################################## # Set up fasta and agp with UCSC names (DONE - 2020-02-27 - Angie) mkdir /hive/data/genomes/grcM38P6/ucsc cd /hive/data/genomes/grcM38P6/ucsc # identify sequences not in existing genome db faCount ../genbank/GCA_000001635.8_GRCm38.p6_genomic.fna.gz \ - > faCount.GRCm38.p13.txt + > faCount.GRCm38.p6.txt ~/kent/src/hg/makeDb/doc/mm10.scanAssemblyReport.pl \ /hive/data/genomes/mm10/chrom.sizes \ - faCount.GRCm38.p13.txt ../genbank/GCA_000001635.8_GRCm38.p6_assembly_report.txt \ + faCount.GRCm38.p6.txt ../genbank/GCA_000001635.8_GRCm38.p6_assembly_report.txt \ | grep -w new > new.sequences.list wc -l new.sequences.list #173 new.sequences.list # Extract UCSC-named FASTA for the new sequences cut -f3 new.sequences.list > extract.new.list awk '{printf "s/%s/%s/; ", $3,$1}' new.sequences.list > genbankToUCSC.sed faSomeRecords ../genbank/GCA_000001635.8_GRCm38.p6_genomic.fna.gz extract.new.list stdout \ | sed -e 's/ .*//;' \ | sed -f genbankToUCSC.sed \ | gzip -c > grcM38P6.fa.gz faSize grcM38P6.fa.gz #88102774 bases (1347579 N's 86755195 real 55734044 upper 31021151 lower) in 173 sequences in 1 files #Total size: mean 509264.6 sd 841533.2 min 25407 (chr19_JH584319_alt) max 5956088 (chr6_GL456054_alt) median 250595 #%35.21 masked total, %35.76 masked real # Compare faSize results for whole GCA_000001635.8_GRCm38.p6_genomic.fna.gz # vs. concatenation of mm10 fasta and grcM38P6.fa.gz: faSize ../genbank/GCA_000001635.8_GRCm38.p6_genomic.fna.gz #2818974548 bases (79435853 N's 2739538695 real 1742143537 upper 997395158 lower) in 239 sequences in 1 files #Total size: mean 11794872.6 sd 37961604.4 min 1976 (JH584295.1) max 195471971 (CM000994.2) median 227966 twoBitToFa /hive/data/genomes/mm10/mm10.2bit stdout \ | faSize grcM38P6.fa.gz stdin #2818974548 bases (79435853 N's 2739538695 real 1510001852 upper 1229536843 lower) in 239 sequences in 2 files #Total size: mean 11794872.6 sd 37961604.4 min 1976 (chr4_JH584295_random) max 195471971 (chr1) median 227966 # Good, everything in GCA_000001635.8_GRCm38.p6_genomic.fna.gz is accounted for # between mm10.2bit and grcM38P6.fa.gz # Make UCSC-named AGP: zcat ../genbank/GCA_000001635.8_GRCm38.p6_assembly_structure/*/alt_scaffolds/AGP/alt.scaf.agp.gz \ | grep -Fwf extract.new.list \ | sed -f genbankToUCSC.sed > grcM38P6.agp # construct 2bit file: cd /hive/data/genomes/grcM38P6 faToTwoBit ucsc/grcM38P6.fa.gz grcM38P6.unmasked.2bit twoBitInfo grcM38P6.unmasked.2bit stdout | sort -k2nr > chrom.sizes # take a look at chrom.sizes to verify it looks OK. # Make sure AGP and FASTA/2bit agree: checkAgpAndFa ucsc/grcM38P6.agp grcM38P6.unmasked.2bit | tail -1 #All AGP and FASTA entries agree - both files are valid ############################################################################## # establish config.ra file (DONE - Angie - 2020-02-27) # arguments here are: <db> <clade> <trackDbDir> <assembly_report.txt> cd /hive/data/genomes/grcM38P6 # Must make photoReference.txt first -- copy from mm10 cp /hive/data/genomes/mm10/photoReference.txt . $HOME/kent/src/hg/utils/automation/prepConfig.pl grcM38P6 haplotypes \ - GRCm38.p13 genbank/*_assembly_report.txt > grcM38P6.config.ra + GRCm38.p6 genbank/*_assembly_report.txt > grcM38P6.config.ra # Edit grcM38P6.config.ra to avoid confusion with actual mm10 assemblyDate Sep. 2017 p6 sed -e 's/^/#/' grcM38P6.config.ra ## config parameters for makeGenomeDb.pl: #db grcM38P6 #clade haplotypes #genomeCladePriority 134 #scientificName Mus musculus #commonName House mouse #assemblyDate Sep. 2017 p6 #assemblyLabel Genome Reference Consortium #assemblyShortLabel GRCm38.p6 #orderKey 8695 ## mitochondrial sequence included in refseq release ## mitoAcc AY172335.1 #mitoAcc none #fastaFiles /hive/data/genomes/grcM38P6/ucsc/*.fa.gz #agpFiles /hive/data/genomes/grcM38P6/ucsc/*.agp ## qualFiles none -#dbDbSpeciesDir GRCm38.p13 +#dbDbSpeciesDir GRCm38.p6 #photoCreditURL http://www.jax.org/ #photoCreditName Photo courtesy of The Jackson Laboratory #ncbiGenomeId 52 #ncbiAssemblyId 1198761 #ncbiAssemblyName GRCm38.p6 #ncbiBioProject 20689 #ncbiBioSample notFound #genBankAccessionID GCF_000001635.26 #taxId 10090 ############################################################################## # Initial database build (DONE - 2020-02-27 - Angie) cd /hive/data/genomes/grcM38P6 # AGP and unmasked.2bit are already built and checked, so start at the db step: mkdir jkStuff $HOME/kent/src/hg/utils/automation/makeGenomeDb.pl grcM38P6.config.ra -debug #HgStepManager: executing from step 'seq' through step 'trackDb'. #HgStepManager: executing step 'seq' Thu Feb 27 12:22:44 2020. #seq: looks like this was run successfully already (/cluster/data/grcM38P6/chrom.sizes exists). Either run with -continue agp or some later step, or move aside/remove /cluster/data/grcM38P6/chrom.sizes and run again. # Make chromInfo.tab. mkdir -p bed/chromInfo awk '{print $1 "\t" $2 "\t/gbdb/grcM38P6/grcM38P6.2bit";}' chrom.sizes \ > bed/chromInfo/chromInfo.tab # Make a link to the .agp file where makeGenomeDb.pl expects to find it. ln -s ucsc/grcM38P6.agp . # Skip 'seq' and 'agp' steps because those were done above. time ($HOME/kent/src/hg/utils/automation/makeGenomeDb.pl \ -workhorse=hgwdev -dbHost=hgwdev -fileServer=hgwdev \ -continue=db grcM38P6.config.ra) > db.log 2>&1 & tail -f db.log #real 0m51.150s # Ignore all the "NOTES -- STUFF THAT YOU WILL HAVE TO DO --" stuff because this is # going to be folded into mm10. # Now the gold, gap and gc5BaseBw tracks are built. ############################################################################# # RepeatMasker (DONE - 2020-02-27 - Angie) mkdir /hive/data/genomes/grcM38P6/bed/repeatMasker cd /hive/data/genomes/grcM38P6/bed/repeatMasker time ($HOME/kent/src/hg/utils/automation/doRepeatMasker.pl -buildDir=`pwd` \ -bigClusterHub=ku -dbHost=hgwdev -workhorse=hgwdev \ -smallClusterHub=ku grcM38P6) > do.log 2>&1 & tail -f do.log # *** All done! - Elapsed time: 99m15s egrep "bases|Total|masked" faSize.rmsk.txt \ | fold -w 95 -s | sed -e 's/^/# /;' # 88102774 bases (1347579 N's 86755195 real 47988960 upper 38766235 lower) in 173 sequences in 1 # files # Total size: mean 509264.6 sd 841533.2 min 25407 (chr19_JH584319_alt) max 5956088 # (chr6_GL456054_alt) median 250595 # %44.00 masked total, %44.68 masked real egrep -i "versi|relea" do.log | sed -e 's/^/# /;' # RepeatMasker version development-$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; * featureBits -countGaps grcM38P6 rmsk #38767309 bases of 88102774 (44.002%) in intersection ########################################################################## # running simple repeat (DONE - 2020-02-27 - Angie) mkdir /hive/data/genomes/grcM38P6/bed/simpleRepeat cd /hive/data/genomes/grcM38P6/bed/simpleRepeat # using trf409 6 here like mm10 time ($HOME/kent/src/hg/utils/automation/doSimpleRepeat.pl -buildDir=`pwd` \ -dbHost=hgwdev -workhorse=hgwdev -bigClusterHub=ku -smallClusterHub=ku \ -trf409 6 grcM38P6) > do.log 2>&1 & #real 5m58.157s cat fb.simpleRepeat #3242454 bases of 86820106 (3.735%) in intersection # adding this trfMask to .rmsk.2bit cd /hive/data/genomes/grcM38P6 twoBitMask grcM38P6.rmsk.2bit \ -add bed/simpleRepeat/trfMask.bed grcM38P6.2bit # you can safely ignore the warning about fields >= 13 twoBitToFa grcM38P6.2bit stdout | faSize stdin > faSize.grcM38P6.2bit.txt egrep "bases|Total|masked" faSize.grcM38P6.2bit.txt \ | fold -w 95 -s | sed -e 's/^/# /;' # 88102774 bases (1347579 N's 86755195 real 47911316 upper 38843879 lower) in 173 sequences in 1 # files # Total size: mean 509264.6 sd 841533.2 min 25407 (chr19_JH584319_alt) max 5956088 # (chr6_GL456054_alt) median 250595 # %44.09 masked total, %44.77 masked real # reset the symlink ln -sf `pwd`/grcM38P6.2bit /gbdb/grcM38P6/grcM38P6.2bit ########################################################################## ## WINDOWMASKER (DONE - 2020-02-27 - Angie) mkdir /hive/data/genomes/grcM38P6/bed/windowMasker cd /hive/data/genomes/grcM38P6/bed/windowMasker time ($HOME/kent/src/hg/utils/automation/doWindowMasker.pl -buildDir=`pwd` \ -workhorse=hgwdev -dbHost=hgwdev grcM38P6) > do.log 2>&1 # *** All done ! - Elapsed time: 2m39s featureBits -countGaps grcM38P6 rmsk windowmaskerSdust \ > fb.grcM38P6.rmsk.windowmaskerSdust.txt 2>&1 cat fb.grcM38P6.rmsk.windowmaskerSdust.txt #19004598 bases of 88102774 (21.571%) in intersection # Masking statistics egrep "bases|Total|masked" faSize.grcM38P6.cleanWMSdust.txt \ | fold -w 95 -s | sed -e 's/^/# /;' # 88102774 bases (1347579 N's 86755195 real 63020753 upper 23734442 lower) in 173 sequences in 1 # files # Total size: mean 509264.6 sd 841533.2 min 25407 (chr19_JH584319_alt) max 5956088 # (chr6_GL456054_alt) median 250595 # %26.94 masked total, %27.36 masked real ############################################################################# # cytoBandIdeo - (DONE - 2020-02-27 - Angie) mkdir /hive/data/genomes/grcM38P6/bed/cytoBand cd /hive/data/genomes/grcM38P6/bed/cytoBand makeCytoBandIdeo.csh grcM38P6 ############################################################################# # cpgIslands - (DONE - 2020-02-27 - Angie) mkdir /hive/data/genomes/grcM38P6/bed/cpgIslands cd /hive/data/genomes/grcM38P6/bed/cpgIslands time ($HOME/kent/src/hg/utils/automation/doCpgIslands.pl -dbHost=hgwdev \ -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku grcM38P6) > do.log 2>&1 & # *** All done ! Elapsed time: 1m16s cat fb.grcM38P6.cpgIslandExt.txt #659505 bases of 86820106 (0.760%) in intersection ############################################################################## # genscan - (DONE - 2020-02-27 - Angie) mkdir /hive/data/genomes/grcM38P6/bed/genscan cd /hive/data/genomes/grcM38P6/bed/genscan time ($HOME/kent/src/hg/utils/automation/doGenscan.pl -buildDir=`pwd` \ -workhorse=hgwdev -dbHost=hgwdev -bigClusterHub=ku grcM38P6) > do.log 2>&1 & # *** All done ! Elapsed time: 7m15s cat fb.grcM38P6.genscan.txt #2980902 bases of 86820106 (3.433%) in intersection cat fb.grcM38P6.genscanSubopt.txt #2063609 bases of 86820106 (2.377%) in intersection ############################################################################# # augustus gene track (DONE - 2020-02-27 - Angie) mkdir /hive/data/genomes/grcM38P6/bed/augustus cd /hive/data/genomes/grcM38P6/bed/augustus # There is no mouse or rat in augustus-3.3.1/config/species/, use human. time ($HOME/kent/src/hg/utils/automation/doAugustus.pl -buildDir=`pwd` -bigClusterHub=ku \ -species=human -dbHost=hgwdev -workhorse=hgwdev grcM38P6) > do.log 2>&1 & # *** All done ! Elapsed time: 53m21s cat fb.grcM38P6.augustusGene.txt #2922180 bases of 86820106 (3.366%) in intersection ############################################################################## # Download files (DONE - 2020-02-27 - Angie) cd /hive/data/genomes/grcM38P6 time ($HOME/kent/src/hg/utils/automation/makeDownloads.pl -noChromFiles \ -workhorse=hgwdev grcM38P6) > downloads.log 2>&1 & # *** All done! #real 0m48.201s ############################################################################## # PREPARE LINEAGE SPECIFIC REPEAT FILES FOR LASTZ (DONE - 2020-02-27 - Angie) mkdir /hive/data/genomes/grcM38P6/bed/linSpecRep cd /hive/data/genomes/grcM38P6/bed/linSpecRep # create individual .out files from the master record in ../repeatMasker # cluster job is perhaps overkill for just the patches, but it works mkdir splitOut cat <<'_EOF_' > split.csh #!/bin/csh -fe set C = $1 head -3 ../repeatMasker/grcM38P6.sorted.fa.out > splitOut/${C}.out grep "${C} " ../repeatMasker/grcM38P6.sorted.fa.out >> splitOut/${C}.out _EOF_ chmod +x split.csh cat << '_EOF_' > template #LOOP split.csh $(root1) {check out line+ splitOut/$(root1).out} #ENDLOOP _EOF_ # small ones first: cut -f1 ../../chrom.sizes | tac > chrom.list gensub2 chrom.list single template jobList para make jobList para time #Completed: 173 of 173 jobs #CPU time in finished jobs: 6s 0.11m 0.00h 0.00d 0.000 y #IO & Wait Time: 431s 7.18m 0.12h 0.00d 0.000 y #Average job time: 3s 0.04m 0.00h 0.00d #Longest finished job: 5s 0.08m 0.00h 0.00d #Submission to last job: 19s 0.32m 0.01h 0.00d # now, we can date and process each of those .out files # constructing the mouseSpecific set of repeats # this means repeats found in mouse, and not in others # using human here for 'others' is good enough, a variety # of other species could be used (dog cow etc) where they all # produce the same result mkdir dateRepeats cd dateRepeats cat << '_EOF_' > mkLSR #!/bin/bash set -beEu -o pipefail seq=$1 rm -f $seq.out_homo-sapiens ln -sf ../splitOut/$seq.out . /scratch/data/RepeatMasker/DateRepeats $seq.out -query 'mus musculus' -comp human rm $seq.out mkdir -p ../mouseSpecific /cluster/bin/scripts/extractRepeats 1 $seq.out_homo-sapiens \ > ../mouseSpecific/$seq.out.spec _EOF_ chmod +x mkLSR cat << '_EOF_' > template #LOOP ./mkLSR $(path1) {check out line+ ../mouseSpecific/$(path1).out.spec} #ENDLOOP _EOF_ gensub2 ../chrom.list single template jobList para make jobList para time #Completed: 173 of 173 jobs #CPU time in finished jobs: 3418s 56.96m 0.95h 0.04d 0.000 y #IO & Wait Time: 481s 8.02m 0.13h 0.01d 0.000 y #Average job time: 23s 0.38m 0.01h 0.00d #Longest finished job: 27s 0.45m 0.01h 0.00d #Submission to last job: 140s 2.33m 0.04h 0.00d # We also need the nibs for blastz runs with lineage specific repeats mkdir /hive/data/genomes/grcM38P6/bed/nibs cd /hive/data/genomes/grcM38P6/bed/nibs cut -f1 ../../chrom.sizes | while read C do twoBitToFa -seq=${C} ../../grcM38P6.2bit stdout \ | faToNib -softMask stdin ${C}.nib echo "${C} done" done # verify nothing lost cat ../../chrom.sizes \ | awk '{printf "nibFrag -masked %s.nib 0 %d + stdout\n", $1, $2}' \ | sh | faSize stdin #88102774 bases (1347579 N's 86755195 real 47911316 upper 38843879 lower) in 173 sequences in 1 files #Total size: mean 509264.6 sd 841533.2 min 25407 (chr19_JH584319_alt.nib:0-25407) max 5956088 (chr6_GL456054_alt.nib:0-5956088) median 250595 #N count: mean 7789.5 sd 36082.3 #U count: mean 276944.0 sd 482134.1 #L count: mean 224531.1 sd 347440.4 #%44.09 masked total, %44.77 masked real mkdir -p /hive/data/staging/data/grcM38P6/nib rsync -a --progress ./ /hive/data/staging/data/grcM38P6/nib rsync -a --progress /hive/data/genomes/grcM38P6/{grcM38P6.2bit,chrom.sizes} \ /hive/data/staging/data/grcM38P6/ ##############################################################################