# for emacs: -*- mode: sh; -*- ############################################################################## # hg38 patch 5 build ############################################################################## ## download sequence, prepare files (DONE - 2015-12-03 - Jonathan) ############################################################################## mkdir /hive/data/genomes/hg38/bed/hg38Patch5 cd /hive/data/genomes/hg38/bed/hg38Patch5 mkdir genbank cd genbank time rsync -L -a -P \ rsync://ftp.ncbi.nlm.nih.gov/genomes/genbank/vertebrate_mammalian/Homo_sapiens/all_assembly_versions/GCA_000001405.20_GRCh38.p5/ ./ # real 5m8.815s # appears to be the entire assembly: faSize GCA_000001405.20_GRCh38.p5_genomic.fna.gz # 3230538373 bases (161368466 N's 3069169907 real 1902976135 upper 1166193772 # lower) in 517 sequences in 1 files # Total size: mean 6248623.5 sd 29673635.8 min 970 (KI270394.1) max 248956422 # (CM000663.2) median 164170 # %36.10 masked total, %38.00 masked real # so the question is, what is new here compared to what we have in hg38 cd /hive/data/genomes/hg38/bed/hg38Patch5 time faCount genbank/GCA_000001405.20_GRCh38.p5_genomic.fna.gz \ > faCount.GRCH38.p5.txt # real 1m12.113s ~/kent/src/hg/makeDb/doc/hg38/scanAssemblyReport.pl ../../chrom.sizes \ faCount.GRCH38.p5.txt genbank/GCA_000001405.20_GRCh38.p5_assembly_report.txt \ | grep new | sed -e 's/^/# /' # there are 62 new sequences: # chr1_KN538361v1_fix 305542 KN538361.1 new # chr1_KQ031383v1_fix 467143 KQ031383.1 new # chr1_KQ458383v1_alt 349938 KQ458383.1 new # chr1_KN196472v1_fix 186494 KN196472.1 new # chr1_KN196473v1_fix 166200 KN196473.1 new # chr1_KQ458382v1_alt 141019 KQ458382.1 new # chr1_KN196474v1_fix 122022 KN196474.1 new # chr1_KN538360v1_fix 460100 KN538360.1 new # chr1_KQ458384v1_alt 212205 KQ458384.1 new # chr2_KN538362v1_fix 208149 KN538362.1 new # chr2_KN538363v1_fix 365499 KN538363.1 new # chr2_KQ031384v1_fix 481245 KQ031384.1 new # chr3_KN196475v1_fix 451168 KN196475.1 new # chr3_KN196476v1_fix 305979 KN196476.1 new # chr3_KN538364v1_fix 415308 KN538364.1 new # chr3_KQ031385v1_fix 373699 KQ031385.1 new # chr3_KQ031386v1_fix 165718 KQ031386.1 new # chr4_KQ090013v1_alt 90922 KQ090013.1 new # chr4_KQ090014v1_alt 163749 KQ090014.1 new # chr4_KQ090015v1_alt 236512 KQ090015.1 new # chr5_KN196477v1_alt 139087 KN196477.1 new # chr6_KQ090017v1_alt 82315 KQ090017.1 new # chr6_KN196478v1_fix 268330 KN196478.1 new # chr6_KQ031387v1_fix 320750 KQ031387.1 new # chr6_KQ090016v1_fix 245716 KQ090016.1 new # chr7_KQ031388v1_fix 179932 KQ031388.1 new # chr9_KQ090018v1_alt 163882 KQ090018.1 new # chr9_KQ090019v1_alt 134099 KQ090019.1 new # chr9_KN196479v1_fix 330164 KN196479.1 new # chr10_KN538367v1_fix 420164 KN538367.1 new # chr10_KQ090020v1_alt 185507 KQ090020.1 new # chr10_KN196480v1_fix 277797 KN196480.1 new # chr10_KN538365v1_fix 14347 KN538365.1 new # chr10_KN538366v1_fix 85284 KN538366.1 new # chr10_KQ090021v1_fix 264545 KQ090021.1 new # chr11_KN538368v1_alt 203552 KN538368.1 new # chr11_KN196481v1_fix 108875 KN196481.1 new # chr11_KQ090022v1_fix 181958 KQ090022.1 new # chr12_KQ090023v1_alt 109323 KQ090023.1 new # chr12_KN196482v1_fix 211377 KN196482.1 new # chr12_KN538369v1_fix 541038 KN538369.1 new # chr12_KN538370v1_fix 86533 KN538370.1 new # chr13_KN538372v1_fix 356766 KN538372.1 new # chr13_KQ090024v1_alt 168146 KQ090024.1 new # chr13_KN196483v1_fix 35455 KN196483.1 new # chr13_KN538373v1_fix 148762 KN538373.1 new # chr13_KQ090025v1_alt 123480 KQ090025.1 new # chr13_KN538371v1_fix 206320 KN538371.1 new # chr15_KN538374v1_fix 4998962 KN538374.1 new # chr15_KQ031389v1_alt 2365364 KQ031389.1 new # chr16_KQ031390v1_alt 169136 KQ031390.1 new # chr16_KQ090026v1_alt 59016 KQ090026.1 new # chr16_KQ090027v1_alt 267463 KQ090027.1 new # chr18_KQ458385v1_alt 205101 KQ458385.1 new # chr18_KQ090028v1_fix 407387 KQ090028.1 new # chr19_KN196484v1_fix 370917 KN196484.1 new # chr19_KQ458386v1_fix 405389 KQ458386.1 new # chr22_KN196485v1_alt 156562 KN196485.1 new # chr22_KN196486v1_alt 153027 KN196486.1 new # chr22_KQ458387v1_alt 155930 KQ458387.1 new # chr22_KQ458388v1_alt 174749 KQ458388.1 new # chrY_KN196487v1_fix 101150 KN196487.1 new # how much sequence: ~/kent/src/hg/makeDb/doc/hg38/scanAssemblyReport.pl ../../chrom.sizes \ faCount.GRCH38.p5.txt genbank/GCA_000001405.20_GRCh38.p5_assembly_report.txt \ | grep new | awk '{sum += $2; printf "%d\t%s\n", sum, $0}' | tail # 21252268 chrY_KN196487v1_fix 101150 KN196487.1 new ~/kent/src/hg/makeDb/doc/hg38/scanAssemblyReport.pl ../../chrom.sizes \ faCount.GRCH38.p5.txt genbank/GCA_000001405.20_GRCh38.p5_assembly_report.txt \ | grep new > new.sequences.list cut -f3 new.sequences.list > extract.new.list awk '{printf "s/%s/%s/; ", $3,$1}' new.sequences.list > genbankToUCSC.sed ~/kent/src/hg/makeDb/doc/hg38/scanAssemblyReport.pl ../../chrom.sizes \ faCount.GRCH38.p5.txt genbank/GCA_000001405.20_GRCh38.p5_assembly_report.txt \ | grep -v new > existing.sequences.list cut -f3 existing.sequences.list > extract.exist.list faSomeRecords genbank/GCA_000001405.20_GRCh38.p5_genomic.fna.gz \ extract.new.list stdout | sed -e 's/ .*//;' | \ sed -f genbankToUCSC.sed | gzip -c > hg38Patch5.fa.gz faSomeRecords genbank/GCA_000001405.20_GRCh38.p5_genomic.fna.gz \ extract.exist.list stdout | sed -e 's/ .*//;' | gzip -c > existing.fa.gz # verify same amount of sequence here as hg38: faSize existing.fa.gz # 3209286105 bases (159970322 N's 3049315783 real 1890811945 upper # 1158503838 lower) in 455 sequences in 1 files # Total size: mean 7053376.1 sd 31548372.6 min 970 (KI270394.1) # max 248956422 (CM000663.2) median 161218 # %36.10 masked total, %37.99 masked real # hg38 has different masking head -1 ../../faSize.hg38.2bit.txt # 3209286105 bases (159970322 N's 3049315783 real 1460684798 upper 1588630985 lower) in 455 sequences in 1 files # verify correct amount of patch5 sequence here: faSize hg38Patch5.fa.gz # 21252268 bases (1398144 N's 19854124 real 12164190 upper 7689934 lower) in # 62 sequences in 1 files # Total size: mean 342778.5 sd 670744.1 min 14347 (chr10_KN538365v1_fix) max # 4998962 (chr15_KN538374v1_fix) median 205101 # N count: mean 22550.7 sd 170147.2 # U count: mean 196196.6 sd 400866.2 # L count: mean 124031.2 sd 222508.3 # %36.18 masked total, %38.73 masked real # this is the same total obtained before: # 21252268 chrY_KN196487v1_fix 101150 KN196487.1 new # and both together should equal the original full patch5 sequence zcat existing.fa.gz hg38Patch5.fa.gz | faSize stdin # 3230538373 bases (161368466 N's 3069169907 real 1902976135 upper # 1166193772 lower) in 517 sequences in 1 files # same as was measured in GCA_000001405.20_GRCh38.p5_genomic.fna.gz: # 3230538373 bases (161368466 N's 3069169907 real 1902976135 upper 1166193772 # lower) in 517 sequences in 1 files # construct locations file: ~/kent/src/hg/makeDb/doc/hg38/regionScan.pl extract.new.list \ genbank/GCA_000001405.20_GRCh38.p5_assembly_regions.txt \ > patchLocations.bed # separate haplotypes from fix patches for two tracks: grep -v fix patchLocations.bed | sed -e 's/_alt//;' \ | sed -e 's/\tchr.*_/\t/;' | sed -e 's/v/./;' > hg38Patch5Haplotypes.bed hgLoadBed -type=bed4 hg38 hg38Patch5Haplotypes hg38Patch5Haplotypes.bed # Read 24 elements of size 4 from hg38Patch5Haplotypes.bed grep fix patchLocations.bed | sed -e 's/_fix//;' \ | sed -e 's/\tchr.*_/\t/;' | sed -e 's/v\([0-9]\)$/.\1/;' \ > hg38Patch5Patches.bed hgLoadBed -type=bed4 hg38 hg38Patch5Patches hg38Patch5Patches.bed # Read 38 elements of size 4 from hg38Patch5Patches.bed # construct 2bit file: faToTwoBit hg38Patch5.fa.gz hg38Patch5.unmasked.2bit twoBitInfo hg38Patch5.unmasked.2bit stdout | sort -k2nr > hg38Patch5.chrom.sizes # take a look at that to verify it looks OK: cat hg38Patch5.chrom.sizes | sed -e 's/^/# /;' # chr15_KN538374v1_fix 4998962 # chr15_KQ031389v1_alt 2365364 # chr12_KN538369v1_fix 541038 # chr2_KQ031384v1_fix 481245 # chr1_KQ031383v1_fix 467143 # chr1_KN538360v1_fix 460100 # chr3_KN196475v1_fix 451168 # chr10_KN538367v1_fix 420164 # chr3_KN538364v1_fix 415308 # chr18_KQ090028v1_fix 407387 # chr19_KQ458386v1_fix 405389 # chr3_KQ031385v1_fix 373699 # chr19_KN196484v1_fix 370917 # chr2_KN538363v1_fix 365499 # chr13_KN538372v1_fix 356766 # chr1_KQ458383v1_alt 349938 # chr9_KN196479v1_fix 330164 # chr6_KQ031387v1_fix 320750 # chr3_KN196476v1_fix 305979 # chr1_KN538361v1_fix 305542 # chr10_KN196480v1_fix 277797 # chr6_KN196478v1_fix 268330 # chr16_KQ090027v1_alt 267463 # chr10_KQ090021v1_fix 264545 # chr6_KQ090016v1_fix 245716 # chr4_KQ090015v1_alt 236512 # chr1_KQ458384v1_alt 212205 # chr12_KN196482v1_fix 211377 # chr2_KN538362v1_fix 208149 # chr13_KN538371v1_fix 206320 # chr18_KQ458385v1_alt 205101 # chr11_KN538368v1_alt 203552 # chr1_KN196472v1_fix 186494 # chr10_KQ090020v1_alt 185507 # chr11_KQ090022v1_fix 181958 # chr7_KQ031388v1_fix 179932 # chr22_KQ458388v1_alt 174749 # chr16_KQ031390v1_alt 169136 # chr13_KQ090024v1_alt 168146 # chr1_KN196473v1_fix 166200 # chr3_KQ031386v1_fix 165718 # chr9_KQ090018v1_alt 163882 # chr4_KQ090014v1_alt 163749 # chr22_KN196485v1_alt 156562 # chr22_KQ458387v1_alt 155930 # chr22_KN196486v1_alt 153027 # chr13_KN538373v1_fix 148762 # chr1_KQ458382v1_alt 141019 # chr5_KN196477v1_alt 139087 # chr9_KQ090019v1_alt 134099 # chr13_KQ090025v1_alt 123480 # chr1_KN196474v1_fix 122022 # chr12_KQ090023v1_alt 109323 # chr11_KN196481v1_fix 108875 # chrY_KN196487v1_fix 101150 # chr4_KQ090013v1_alt 90922 # chr12_KN538370v1_fix 86533 # chr10_KN538366v1_fix 85284 # chr6_KQ090017v1_alt 82315 # chr16_KQ090026v1_alt 59016 # chr13_KN196483v1_fix 35455 # chr10_KN538365v1_fix 14347 zcat genbank/GCA_000001405.20_GRCh38.p5_assembly_structure/PATCHES/alt_scaffolds/AGP/alt.scaf.agp.gz \ | sed -f genbankToUCSC.sed > hg38Patch5.agp checkAgpAndFa hg38Patch5.agp hg38Patch5.unmasked.2bit | tail -1 # All AGP and FASTA entries agree - both files are valid ############################################################################# # build hg38Patch5 database (DONE - 2015-12-03 - Jonathan) # need this database for netClass operations during the chain/net # construction mkdir /hive/data/genomes/hg38Patch5 cd /hive/data/genomes/hg38Patch5 mkdir /gbdb/hg38Patch5 ln -s /hive/data/genomes/hg38/bed/hg38Patch5/hg38Patch5.unmasked.2bit ./ ln -s /hive/data/genomes/hg38/bed/hg38Patch5/hg38Patch5.agp ./ twoBitInfo hg38Patch5.unmasked.2bit stdout | sort -k2nr > chrom.sizes mkdir -p bed/chromInfo awk '{printf "%s\t%d\t/gbdb/hg38Patch5/hg38Patch5.2bit\n", $1, $2}' \ chrom.sizes > bed/chromInfo/chromInfo.tab hgsql -e 'create database hg38Patch5;' hg38 hgsql hg38Patch5 < $HOME/kent/src/hg/lib/grp.sql hgLoadSqlTab hg38Patch5 chromInfo $HOME/kent/src/hg/lib/chromInfo.sql \ bed/chromInfo/chromInfo.tab hgGoldGapGl -noGl hg38Patch5 hg38Patch5.agp featureBits -or -countGaps hg38Patch5 gold gap # 21252268 bases of 21252268 (100.000%) in intersection hgsql hgcentraltest -e 'INSERT INTO dbDb (name, description, nibPath, organism, defaultPos, active, orderKey, genome, scientificName, htmlPath, hgNearOk, hgPbOk, sourceName, taxId) VALUES ("hg38Patch5", "Sep. 2015", "/gbdb/hg38Patch5", "GRCh38.p5", "chr1_KN538360v1_fix:1-460100", 1, 7754, "GRCh38.p5", "Homo sapiens", "/gbdb/hg38Patch5/html/description.html", 0, 0, "GRCh38 patch 5 Genome Reference Consortium Human Reference 38", 9606); INSERT INTO defaultDb (genome, name) VALUES ("GRCh38.p5", "hg38Patch5"); INSERT INTO genomeClade (genome, clade, priority) VALUES ("GRCh38.p5", "haplotypes", 134);' mkdir html # copy description.html from hg38Patch2/html/description.html # edit to update for Patch5 mkdir -p /hive/data/genomes/hg38Patch5/bed/gc5Base hgGcPercent -wigOut -doGaps -file=stdout -win=5 -verbose=0 hg38Patch5 \ hg38Patch5.unmasked.2bit | wigEncode stdin bed/gc5Base/gc5Base.{wig,wib} # Converted stdin, upper limit 100.00, lower limit 0.00 mkdir /gbdb/hg38Patch5/wib ln -s `pwd`/bed/gc5Base/gc5Base.wib /gbdb/hg38Patch5/wib hgLoadWiggle -pathPrefix=/gbdb/hg38Patch5/wib hg38Patch5 gc5Base \ bed/gc5Base/gc5Base.wig mkdir /hive/data/genomes/hg38Patch5/bed/repeatMasker cd /hive/data/genomes/hg38Patch5/bed/repeatMasker time doRepeatMasker.pl -bigClusterHub=ku \ -workhorse=hgwdev -dbHost=hgwdev -buildDir=`pwd` hg38Patch5 > do.log 2>&1 # real 48m15.670s mkdir /hive/data/genomes/hg38Patch5/bed/simpleRepeat cd /hive/data/genomes/hg38Patch5/bed/simpleRepeat time (doSimpleRepeat.pl -bigClusterHub=ku -workhorse=hgwdev \ -smallClusterHub=ku -buildDir=`pwd` hg38Patch5) > do.log 2>&1 # real 6m33.955s # the simpleRepeat procedure fails in the cleanup step since there # is no TrfPart directory mkdir /hive/data/genomes/hg38Patch5/bed/windowMasker cd /hive/data/genomes/hg38Patch5/bed/windowMasker time (doWindowMasker.pl -buildDir=`pwd` -workhorse=hgwdev \ -dbHost=hgwdev hg38Patch5) > do.log 2>&1 cd /hive/data/genomes/hg38Patch5 twoBitMask hg38Patch5.rmsk.2bit \ -add bed/simpleRepeat/trfMask.bed hg38Patch5.2bit twoBitToFa hg38Patch5.2bit stdout | faSize stdin # 21252268 bases (1398144 N's 19854124 real 9223467 upper 10630657 lower) # in 62 sequences in 1 files # Total size: mean 342778.5 sd 670744.1 min 14347 (chr10_KN538365v1_fix) # max 4998962 (chr15_KN538374v1_fix) median 205101 # %50.02 masked total, %53.54 masked real ############################################################################# # lastz alignments to hg38 (DONE - 2015-12-04 - Jonathan) ############################################################################# mkdir /hive/data/genomes/hg38/bed/hg38Patch5/lastzHg38.2015-12-03 cd /hive/data/genomes/hg38/bed/hg38Patch5/lastzHg38.2015-12-03 cat << '_EOF_' > DEF BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz # human vs human BLASTZ=lastz # maximum M allowed with lastz is only 254 BLASTZ_M=254 # lastz does not like the O= and E= lines in the matrix file BLASTZ_Q=/scratch/data/blastz/human_chimp.v2.q BLASTZ_O=600 BLASTZ_E=150 # other parameters from hg18 vs venter1 lastz on advice from Webb BLASTZ_K=10000 BLASTZ_Y=15000 BLASTZ_T=2 # TARGET: Human Hg38Patch5 SEQ1_DIR=/hive/data/genomes/hg38/bed/hg38Patch5/hg38Patch5.unmasked.2bit SEQ1_LEN=/hive/data/genomes/hg38/bed/hg38Patch5/hg38Patch5.chrom.sizes SEQ1_CHUNK=10000000 SEQ1_LAP=10000 SEQ1_IN_CONTIGS=0 SEQ1_LIMIT=1 # QUERY: Human Hg38 #SEQ2_DIR=/scratch/data/hg38/hg38.2bit SEQ2_DIR=/hive/data/genomes/hg38/hg38.unmasked.2bit SEQ2_LEN=/scratch/data/hg38/chrom.sizes SEQ2_CTGDIR=/hive/data/genomes/hg38/bed/hg38Patch5/hg38Bits.2bit SEQ2_CTGLEN=/hive/data/genomes/hg38/bed/hg38Patch5/hg38Bits.chrom.sizes SEQ2_LIFT=/hive/data/genomes/hg38/bed/hg38Patch5/hg38Bits.lift SEQ2_CHUNK=10000000 SEQ2_LAP=0 SEQ2_IN_CONTIGS=0 SEQ2_LIMIT=1 BASE=/hive/data/genomes/hg38/bed/hg38Patch5/lastzHg38.2015-12-03 TMPDIR=/dev/shm '_EOF_' # << happy emacs # prepare bits of hg38 sequence to lastz align to the patches, # this is selecting out the specific section of hg38 where the patch # is supposed to match, and setting up lastz parameters rm -fr hg38Bits run.blastz run.blastz/tParts run.blastz/qParts psl \ ../hg38Bits.lift mkdir -p hg38Bits run.blastz run.blastz/tParts run.blastz/qParts psl cut -f4 ../patchLocations.bed | while read FIX do chr=`grep "${FIX}" ../patchLocations.bed | cut -f1` start=`grep "${FIX}" ../patchLocations.bed | cut -f2` end=`grep "${FIX}" ../patchLocations.bed | cut -f3` bitSize=`echo ${end} ${start} | awk '{printf "%d", $1-$2}'` chrSize=`grep -w "${chr}" ../../../chrom.sizes | cut -f2` fixSize=`grep "${FIX}" ../hg38Patch5.chrom.sizes | cut -f2` echo ${chr}:${start}-${end} vs. ${FIX}:0-${fixSize} 1>&2 twoBitToFa /hive/data/genomes/hg38/hg38.unmasked.2bit:${chr}:${start}-${end} stdout \ | sed -e "s/${chr}:/${FIX}_/g" > hg38Bits/${FIX}.fa fixName=`head -1 hg38Bits/${FIX}.fa | sed -e 's/>//;'` echo -e "${start}\t${fixName}\t${fixSize}\t${chr}\t${chrSize}" 1>&2 echo -e "${start}\t${fixName}\t${fixSize}\t${chr}\t${chrSize}" >> ../hg38Bits.lift echo -e "/hive/data/genomes/hg38/bed/hg38Patch5/hg38Bits.2bit:${fixName}:0-${bitSize}" 1>&2 echo -e "/hive/data/genomes/hg38/bed/hg38Patch5/hg38Bits.2bit:${fixName}:0-${bitSize}" > run.blastz/qParts/${fixName}.lst echo -e "/hive/data/genomes/hg38/bed/hg38Patch5/hg38Patch5.unmasked.2bit:${FIX}:0-${fixSize}" > run.blastz/tParts/${fixName}.lst echo -e "/cluster/bin/scripts/blastz-run-ucsc -outFormat psl tParts/${fixName}.lst qParts/${fixName}.lst ../DEF {check out exists ../psl/${fixName}.psl}" 1>&2 echo -e "/cluster/bin/scripts/blastz-run-ucsc -outFormat psl tParts/${fixName}.lst qParts/${fixName}.lst ../DEF {check out exists ../psl/${fixName}.psl}" >> run.blastz/jobList done faToTwoBit hg38Bits/*.fa ../hg38Bits.2bit twoBitInfo ../hg38Bits.2bit stdout | sort -k2n > ../hg38Bits.chrom.sizes ssh ku cd /hive/data/genomes/hg38/bed/hg38Patch5/lastzHg38.2015-12-03/run.blastz para create jobList para try ... check ... push ... etc para time > run.time # Completed: 62 of 62 jobs # CPU time in finished jobs: 60s 1.00m 0.02h 0.00d 0.000 y # IO & Wait Time: 174s 2.90m 0.05h 0.00d 0.000 y # Average job time: 4s 0.06m 0.00h 0.00d # Longest finished job: 16s 0.27m 0.00h 0.00d # Submission to last job: 59s 0.98m 0.02h 0.00d # put together the individual results mkdir pslParts cat psl/chr*.psl | gzip -c > pslParts/hg38Patch5.hg38.psl.gz # constructing a chain from those results mkdir -p /hive/data/genomes/hg38/bed/hg38Patch5/lastzHg38.2015-12-03/axtChain/run cd /hive/data/genomes/hg38/bed/hg38Patch5/lastzHg38.2015-12-03/axtChain/run time zcat ../../pslParts/hg38Patch5.hg38.psl.gz \ | axtChain -psl -verbose=0 -scoreScheme=/scratch/data/blastz/human_chimp.v2.q -minScore=2000 -linearGap=medium stdin \ /hive/data/genomes/hg38/bed/hg38Patch5/hg38Patch5.unmasked.2bit \ /hive/data/genomes/hg38/bed/hg38Patch5/hg38Bits.2bit \ stdout \ | chainAntiRepeat /hive/data/genomes/hg38/bed/hg38Patch5/hg38Patch5.unmasked.2bit \ /hive/data/genomes/hg38/bed/hg38Patch5/hg38Bits.2bit \ stdin hg38Patch5.hg38.preLift.chain # real 0m1.601s liftUp -chainQ hg38Patch5.hg38.lifted.chain \ ../../../hg38Bits.lift carry hg38Patch5.hg38.preLift.chain # constructing the net files: cd /hive/data/genomes/hg38/bed/hg38Patch5/lastzHg38.2015-12-03/axtChain chainMergeSort run/hg38Patch5.hg38.lifted.chain \ | gzip -c > hg38Patch5.hg38.all.chain.gz chainSplit chain hg38Patch5.hg38.all.chain.gz # Make nets ("noClass", i.e. without rmsk/class stats which are added later): time chainPreNet hg38Patch5.hg38.all.chain.gz \ ../../hg38Patch5.chrom.sizes \ /hive/data/genomes/hg38/chrom.sizes stdout \ | chainNet stdin -minSpace=1 ../../hg38Patch5.chrom.sizes \ /hive/data/genomes/hg38/chrom.sizes stdout /dev/null \ | netSyntenic stdin noClass.net # real 0m0.452s hgLoadChain -tIndex hg38Patch5 chainHg38 hg38Patch5.hg38.all.chain.gz featureBits hg38Patch5 chainHg38Link # 18998845 bases of 19854224 (95.692%) in intersection netClass -verbose=0 -noAr noClass.net hg38Patch5 hg38 hg38Patch5.hg38.net netFilter -minGap=10 hg38Patch5.hg38.net \ | hgLoadNet -verbose=0 hg38Patch5 netHg38 stdin # Make liftOver chains: netChainSubset -verbose=0 noClass.net hg38Patch5.hg38.all.chain.gz stdout \ | chainStitchId stdin stdout | gzip -c > hg38Patch5.hg38.over.chain.gz # Make axtNet for download: one .axt per hg38Patch5 seq. netSplit noClass.net net cd .. mkdir -p axtNet # beware, tcsh scripting here: foreach f (axtChain/net/*.net) netToAxt $f axtChain/chain/$f:t:r.chain \ ../hg38Patch5.unmasked.2bit \ /hive/data/genomes/hg38/hg38.unmasked.2bit stdout \ | axtSort stdin stdout \ | gzip -c > axtNet/$f:t:r.hg38Patch5.hg38.net.axt.gz end # Make mafNet for multiz: one .maf per hg38Patch5 seq. mkdir -p mafNet # beware, tcsh scripting here: foreach f (axtNet/*.hg38Patch5.hg38.net.axt.gz) axtToMaf -tPrefix=hg38Patch5. -qPrefix=hg38. $f \ ../hg38Patch5.chrom.sizes \ /hive/data/genomes/hg38/chrom.sizes \ stdout \ | gzip -c > mafNet/$f:t:r:r:r:r:r.maf.gz end ############################################################################# # run this same business with hg38 as target, Patch5 sequence as query # (DONE - 2015-12-16 - Jonathan) mkdir /hive/data/genomes/hg38/bed/hg38Patch5/lastzHg38Patch5.2015-12-04 cd /hive/data/genomes/hg38/bed/hg38Patch5/lastzHg38Patch5.2015-12-04 cat << '_EOF_' > DEF # human vs human BLASTZ=lastz # maximum M allowed with lastz is only 254 BLASTZ_M=254 # lastz does not like the O= and E= lines in the matrix file BLASTZ_Q=/scratch/data/blastz/human_chimp.v2.q BLASTZ_O=600 BLASTZ_E=150 # other parameters from hg18 vs venter1 lastz on advice from Webb BLASTZ_K=10000 BLASTZ_Y=15000 BLASTZ_T=2 # TARGET: Human Hg38 SEQ1_DIR=/hive/data/genomes/hg38/hg38.unmasked.2bit SEQ1_LEN=/scratch/data/hg38/chrom.sizes SEQ1_CTGDIR=/hive/data/genomes/hg38/bed/hg38Patch5/hg38Bits.2bit SEQ1_CTGLEN=/hive/data/genomes/hg38/bed/hg38Patch5/hg38Bits.chrom.sizes SEQ1_LIFT=/hive/data/genomes/hg38/bed/hg38Patch5/hg38Bits.lift SEQ1_CHUNK=10000000 SEQ1_LAP=10000 SEQ1_IN_CONTIGS=0 SEQ1_LIMIT=1 # QUERY: Human Hg38Patch5 SEQ2_DIR=/hive/data/genomes/hg38/bed/hg38Patch5/hg38Patch5.unmasked.2bit SEQ2_LEN=/hive/data/genomes/hg38/bed/hg38Patch5/hg38Patch5.chrom.sizes SEQ2_CHUNK=10000000 SEQ2_LAP=0 SEQ2_IN_CONTIGS=0 SEQ2_LIMIT=1 BASE=/hive/data/genomes/hg38/bed/hg38Patch5/lastzHg38Patch5.2015-12-04 TMPDIR=/dev/shm '_EOF_' # << happy emacs rm -f ../hg38Bits.lift rm -fr hg38Bits run.blastz psl mkdir -p hg38Bits run.blastz/tParts run.blastz/qParts psl cut -f4 ../patchLocations.bed | while read FIX do chr=`grep "${FIX}" ../patchLocations.bed | cut -f1` start=`grep "${FIX}" ../patchLocations.bed | cut -f2` end=`grep "${FIX}" ../patchLocations.bed | cut -f3` bitSize=`echo ${end} ${start} | awk '{printf "%d", $1-$2}'` chrSize=`grep -w "${chr}" ../../../chrom.sizes | cut -f2` fixSize=`grep "${FIX}" ../hg38Patch5.chrom.sizes | cut -f2` echo ${chr}:${start}-${end} vs. ${FIX}:0-${fixSize} 1>&2 twoBitToFa /hive/data/genomes/hg38/hg38.unmasked.2bit:${chr}:${start}-${end} stdout \ | sed -e "s/${chr}:/${FIX}_/g" > hg38Bits/${FIX}.fa fixName=`head -1 hg38Bits/${FIX}.fa | sed -e 's/>//;'` #echo -e "${start}\t${fixName}\t${fixSize}\t${chr}\t${chrSize}" >> ../hg38Bits.lift echo -e "/hive/data/genomes/hg38/bed/hg38Patch5/hg38Bits.2bit:${fixName}:0-${bitSize}" > run.blastz/tParts/${FIX}.lst echo -e "/hive/data/genomes/hg38/bed/hg38Patch5/hg38Patch5.unmasked.2bit:${FIX}:0-${fixSize}" > run.blastz/qParts/${FIX}.lst echo -e "/cluster/bin/scripts/blastz-run-ucsc -outFormat psl tParts/${FIX}.lst qParts/${FIX}.lst ../DEF {check out exists ../psl/${FIX}.psl}" >> run.blastz/jobList done ssh ku cd /hive/data/genomes/hg38/bed/hg38Patch5/lastzHg38Patch5.2015-12-04/run.blastz para create jobList para try ... check ... push ... etc para time # Completed: 62 of 62 jobs # CPU time in finished jobs: 62s 1.03m 0.02h 0.00d 0.000 y # IO & Wait Time: 190s 3.17m 0.05h 0.00d 0.000 y # Average job time: 4s 0.07m 0.00h 0.00d # Longest finished job: 20s 0.33m 0.01h 0.00d # Submission to last job: 35s 0.58m 0.01h 0.00d # put together the individual results cd /hive/data/genomes/hg38/bed/hg38Patch5/lastzHg38Patch5.2015-12-04 mkdir pslParts cat psl/chr*.psl | gzip -c > pslParts/hg38.hg38Patch5.psl.gz # constructing a chain from those results mkdir -p /hive/data/genomes/hg38/bed/hg38Patch5/lastzHg38Patch5.2015-12-04/axtChain/run cd /hive/data/genomes/hg38/bed/hg38Patch5/lastzHg38Patch5.2015-12-04/axtChain/run time zcat ../../pslParts/hg38.hg38Patch5.psl.gz \ | axtChain -psl -verbose=0 -scoreScheme=/scratch/data/blastz/human_chimp.v2.q -minScore=2000 -linearGap=medium stdin \ /hive/data/genomes/hg38/bed/hg38Patch5/hg38Bits.2bit \ /hive/data/genomes/hg38/bed/hg38Patch5/hg38Patch5.unmasked.2bit \ stdout \ | chainAntiRepeat /hive/data/genomes/hg38/bed/hg38Patch5/hg38Bits.2bit \ /hive/data/genomes/hg38/bed/hg38Patch5/hg38Patch5.unmasked.2bit \ stdin hg38.hg38Patch5.preLift.chain # real 0m1.943s liftUp hg38.hg38Patch5.lifted.chain \ ../../../hg38Bits.lift carry hg38.hg38Patch5.preLift.chain # constructing the net files: cd /hive/data/genomes/hg38/bed/hg38Patch5/lastzHg38Patch5.2015-12-04/axtChain chainMergeSort run/hg38.hg38Patch5.lifted.chain \ | gzip -c > hg38.hg38Patch5.all.chain.gz hgLoadChain -tIndex hg38 chainHg38Patch5 hg38.hg38Patch5.all.chain.gz # Loading 4844 chains into hg38.chainHg38Patch5 featureBits hg38 chainHg38Patch5Link # 18975466 bases of 3049335806 (0.622%) in intersection chainSplit chain hg38.hg38Patch5.all.chain.gz # Make nets ("noClass", i.e. without rmsk/class stats which are added later): time chainPreNet hg38.hg38Patch5.all.chain.gz \ /hive/data/genomes/hg38/chrom.sizes \ ../../hg38Patch5.chrom.sizes stdout \ | chainNet stdin -minSpace=1 /hive/data/genomes/hg38/chrom.sizes \ ../../hg38Patch5.chrom.sizes stdout /dev/null \ | netSyntenic stdin noClass.net # real 0m0.443s netClass -verbose=0 -noAr noClass.net hg38 hg38Patch5 hg38.hg38Patch5.net netFilter -minGap=10 hg38.hg38Patch5.net \ | hgLoadNet -verbose=0 hg38 netHg38Patch5 stdin # Make liftOver chains: netChainSubset -verbose=0 noClass.net hg38.hg38Patch5.all.chain.gz stdout \ | chainStitchId stdin stdout | gzip -c > hg38.hg38Patch5.over.chain.gz # Make axtNet for download: one .axt per hg38Patch5 seq. netSplit noClass.net net cd .. mkdir -p axtNet # more tcsh here foreach f (axtChain/net/*.net) netToAxt $f axtChain/chain/$f:t:r.chain \ /hive/data/genomes/hg38/hg38.unmasked.2bit \ ../hg38Patch5.unmasked.2bit stdout \ | axtSort stdin stdout \ | gzip -c > axtNet/$f:t:r.hg38.hg38Patch5.net.axt.gz end # Make mafNet for multiz: one .maf per hg38Patch5 seq. mkdir -p mafNet # tcsh loop again foreach f (axtNet/*.hg38.hg38Patch5.net.axt.gz) axtToMaf -tPrefix=hg38. -qPrefix=hg38Patch5. $f \ /hive/data/genomes/hg38/chrom.sizes \ ../hg38Patch5.chrom.sizes \ stdout \ | gzip -c > mafNet/$f:t:r:r:r:r:r.maf.gz end cd /hive/data/genomes/hg38/bed/hg38Patch5/lastzHg38Patch5.2015-12-04/axtChain mkdir -p queryChains chainSplit -q queryChains hg38.hg38Patch5.all.chain.gz # then run a 'lift over' chain/net on each single one mkdir -p singleLiftOver for F in queryChains/*.chain do C=`basename ${F}` B=`echo ${C} | sed -e "s/.chain//"` chainPreNet -inclHap ${F} /hive/data/genomes/hg38/chrom.sizes \ ../../hg38Patch5.chrom.sizes stdout \ | chainNet -inclHap stdin -minSpace=1 /hive/data/genomes/hg38/chrom.sizes \ ../../hg38Patch5.chrom.sizes singleLiftOver/${B}.raw.net \ /dev/null netSyntenic singleLiftOver/${B}.raw.net singleLiftOver/${B}.noClass.net netFilter -chimpSyn singleLiftOver/${B}.noClass.net > singleLiftOver/${B}.chimpSyn.net netChainSubset -verbose=0 singleLiftOver/${B}.noClass.net \ ${F} stdout \ | chainStitchId stdin stdout > singleLiftOver/${C} echo "${F} -> singleLiftOver/${C}" done # put the chains together into one file chainMergeSort singleLiftOver/chr*.chain | gzip -c \ > hg38.hg38Patch5.single.over.chain.gz # construct psl files from those chains chainToPsl hg38.hg38Patch5.single.over.chain.gz \ /hive/data/genomes/hg38/chrom.sizes \ ../../hg38Patch5.chrom.sizes \ /hive/data/genomes/hg38/hg38.unmasked.2bit \ ../../hg38Patch5.unmasked.2bit \ hg38.hg38Patch5.over.psl # pslCheck reports no errors pslCheck -db=hg38 hg38.hg38Patch5.over.psl # checked: 99 failed: 0 errors: 0 # load this PSL track # this table name prefix altSeqLiftOverPsl is recognized in hgc clicks hgLoadPsl hg38 -table=altSeqLiftOverPslP5 hg38.hg38Patch5.over.psl mkdir /hive/data/genomes/hg38/bed/hg38Patch5/seqExt cd /hive/data/genomes/hg38/bed/hg38Patch5/seqExt twoBitToFa ../hg38Patch5.unmasked.2bit hg38Patch5.fa mkdir -p /gbdb/hg38/hg38Patch5 hg38Patch5 faSplit byname hg38Patch5.fa ./hg38Patch5/ ln -s `pwd`/hg38Patch5/*.fa /gbdb/hg38/hg38Patch5 hgLoadSeq -drop -seqTbl=seqHg38Patch5 -extFileTbl=extHg38Patch5 hg38 \ /gbdb/hg38/hg38Patch5/*.fa #############################################################################