de23dd389f8e8e35c41880a85d74e9838a4df8e4 angie Thu Jun 18 15:11:49 2026 -0700 ssh to hgwdev for commands that need access to hgwdev-only directories, because these scripts run elsewhere now. Tweak shell variables usherDir and friends to make it easier to try out different build directories. diff --git src/hg/utils/otto/rsv/buildTree.sh src/hg/utils/otto/rsv/buildTree.sh index ec5ff126f65..3ab050748b9 100755 --- src/hg/utils/otto/rsv/buildTree.sh +++ src/hg/utils/otto/rsv/buildTree.sh @@ -1,276 +1,275 @@ #!/bin/bash source ~/.bashrc set -beEu -o pipefail # Align INSDC sequences to reference and build two trees, one for RSV-A and one for RSV-B. rsvScriptDir=$(dirname "${BASH_SOURCE[0]}") today=$(date +%F) rsvDir=/hive/data/outside/otto/rsv rsvNcbiDir=$rsvDir/ncbi/ncbi.latest -usherDir=~angie/github/usher -usherSampled=$usherDir/build/usher-sampled -usher=$usherDir/build/usher -matUtils=$usherDir/build/matUtils -matOptimize=$usherDir/build/matOptimize +usherDir=~angie/github/usher/build +usherSampled=$usherDir/usher-sampled +usher=$usherDir/usher +matUtils=$usherDir/matUtils +matOptimize=$usherDir/matOptimize # RSV-A reference: Nextstrain uses KJ627695.1 but RefSeq is NC_038235.1 (M74568) asmAccA=GCF_002815475.1 gbffA=$rsvDir/NC_038235.1.gbff nextcladeNameA=rsv_a refFaA=$rsvDir/NC_038235.1.fa archiveRootA=/hive/users/angie/publicTreesRsvA # RSV-B reference: Nextstrain uses ? but RefSeq is NC_001781.1 (AF013254) asmAccB=GCF_000855545.1 gbffB=$rsvDir/NC_001781.1.gbff nextcladeNameB=rsv_b refFaB=$rsvDir/NC_001781.1.fa archiveRootB=/hive/users/angie/publicTreesRsvB # Filter out branches longer than this so we don't get RSV-A and RSV-B in same final tree maxSubs=1500 maxBranchLen=500 if [[ ! -d $rsvDir/ncbi/ncbi.$today || ! -s $rsvDir/ncbi/ncbi.$today/genbank.fa.xz ]]; then mkdir -p $rsvDir/ncbi/ncbi.$today $rsvScriptDir/getNcbiRsv.sh >& $rsvDir/ncbi/ncbi.$today/getNcbiRsv.log fi buildDir=$rsvDir/build/$today mkdir -p $buildDir cd $buildDir # Make sure the download wasn't truncated without reporting an error: count=$(wc -l < $rsvNcbiDir/metadata.tsv) minSamples=5600 if (( $count < $minSamples )); then echo "*** Too few samples ($count)! Expected at least $minSamples. Halting. ***" exit 1 fi # Use metadata to make a renaming file cat $rsvNcbiDir/metadata.tsv \ | sed -re 's@([\t /])h?rsv(-?[ab])?/@\1@ig;' \ | sed -re 's@([\t /])[ab]/@\1@ig;' \ | sed -re 's@([\t /])human/@\1@ig;' \ | sed -re 's@([\t /])homo sapiens/@\1@ig;' \ | sed -re 's@Human respiratory syncytial virus nonstructural protein 1, nonstructural protein 2, nucleocapsid protein, phosphoprotein, matrix protein, small hydrophobic protein, glycoprotein, fusion glycoprotein, 22K/M2 protein and L protein mRNA, complete cds@@;' \ > tweakedMetadata.tsv cut -f 1,12 tweakedMetadata.tsv \ | trimWordy.pl \ > accToIdFromTitle.tsv join -t$'\t' <(sort tweakedMetadata.tsv) accToIdFromTitle.tsv \ | perl -wne 'chomp; @w=split(/\t/); my ($acc, $iso, $loc, $date, $str, $tid) = ($w[0], $w[1], $w[3], $w[4], $w[14], $w[15]); if (! defined $str) { $str = ""; } my $name = $str ? $str : $iso ? $iso : $tid ? $tid : ""; my $country = $loc; $country =~ s/:.*//; my $COU = $country; $COU =~ s/^(\w{3}).*/$1/; $COU = uc($COU); if ($country eq "United Kingdom") { $COU = "UK"; } if ($name !~ /$country/ && $name !~ /\b$COU\b/ && $name ne "") { $name = "$country/$name"; } $name =~ s/[,;]//g; my $year = $date; $year =~ s/-.*//; my $year2 = $year; $year2 =~ s/^\d{2}(\d{2})$/$1/; if ($name ne "" && $name !~ /$year/ && $name !~ /\/$year2$/) { $name = "$name/$year"; } if ($date eq "") { $date = "?"; } my $fullName = $name ? "$name|$acc|$date" : "$acc|$date"; $fullName =~ s/[ ,:()]/_/g; print "$acc\t$fullName\n";' \ > renaming.tsv # This builds the whole tree from scratch! Eventually we'll want to add only the new sequences # to yesterday's tree. echo '()' > emptyTree.nwk for aOrB in A B; do if [[ $aOrB == "A" ]]; then refFa=$refFaA gbff=$gbffA asmAcc=$asmAccA archiveRoot=$archiveRootA nextcladeName=$nextcladeNameA else refFa=$refFaB gbff=$gbffB asmAcc=$asmAccB archiveRoot=$archiveRootB nextcladeName=$nextcladeNameB fi # Run nextclade to get clade assignments -- but not alignments because we need alignments # to RefSeqs not nextclade's chosen references. nextclade dataset get --name $nextcladeName --output-zip $nextcladeName.zip time nextclade run \ -D $nextcladeName.zip \ -j 30 \ --retry-reverse-complement true \ --output-tsv nextclade.rsv$aOrB.tsv \ $rsvDir/ncbi/ncbi.$today/genbank.fa.xz \ >& nextclade.$aOrB.log # Run nextalign with RefSeq. nextalign run --input-ref $refFa \ --include-reference \ --jobs 32 \ --output-fasta aligned.$aOrB.fa.xz \ $rsvDir/ncbi/ncbi.$today/genbank.fa.xz \ >& nextalign.log if [[ -s $rsvScriptDir/mask.$aOrB.vcf ]]; then maskCmd="vcfFilter -excludeVcf=$rsvScriptDir/mask.$aOrB.vcf stdin " else maskCmd="cat" fi time faToVcf -verbose=2 -includeNoAltN -excludeFile=$rsvScriptDir/exclude.ids \ <(xzcat aligned.$aOrB.fa.xz) stdout \ | vcfRenameAndPrune stdin renaming.tsv stdout \ | $maskCmd \ | pigz -p 8 \ > all.$aOrB.vcf.gz time $usherSampled -T 16 -A -e 5 \ -t emptyTree.nwk \ -v all.$aOrB.vcf.gz \ -o rsv$aOrB.$today.preFilter.pb\ --optimization_radius 0 --batch_size_per_process 10 \ > usher.addNew.$aOrB.log 2>usher-sampled.$aOrB.stderr # Filter out branches that are so long they must lead to the other subspecies (B or A) $matUtils extract -i rsv$aOrB.$today.preFilter.pb \ --max-branch-length $maxBranchLen \ -O -o rsv$aOrB.$today.preOpt.pb >& tmp.log # Optimize: time $matOptimize -T 16 -r 20 -M 2 -S move_log.$aOrB \ -i rsv$aOrB.$today.preOpt.pb \ -o rsv$aOrB.$today.opt.pb \ >& matOptimize.$aOrB.log # Annotate consortium clades using nextclade assignments and other sources # (nextstrain.org, supplemental table...). function tl { perl -wne 'chomp; @w = split(/\t/, $_, -1); $i = 1; foreach $w (@w) { print "$i\t$w[$i-1]\n"; $i++; }' } cCol=$(head -1 nextclade.rsv$aOrB.tsv | tl | grep -w clade | cut -f 1) subsCol=$(head -1 nextclade.rsv$aOrB.tsv | tl | grep -w totalSubstitutions | cut -f 1) tail -n+2 nextclade.rsv$aOrB.tsv \ | tawk '$'$subsCol' < '$maxSubs' && $'$cCol' != "" {print $2, $'$cCol';}' \ | sed -re 's/unassigned/Unassigned/;' \ | sort > accToCClade join -t$'\t' accToCClade renaming.tsv \ | grep -v Unassigned | cut -f 2,3 | sort \ > cCladeToName.$aOrB if [[ -s $rsvScriptDir/gcc.$aOrB.clade-mutations.tsv ]]; then cladeMuts="-M $rsvScriptDir/gcc.$aOrB.clade-mutations.tsv" else cladeMuts="" fi $matUtils annotate -T 16 -f 0.9 -m 0.1 -i rsv$aOrB.$today.opt.pb \ -c cCladeToName.$aOrB $cladeMuts -o rsv$aOrB.$today.pb \ >& annotate.$aOrB.cClade.log $matUtils summary -i rsv$aOrB.$today.pb -C sample-clades.$aOrB >& tmp.log # Make metadata that uses same names as tree echo -e "strain\tgenbank_accession\tdate\tcountry\tlocation\tlength\thost\tbioproject_accession\tbiosample_accession\tsra_accession\tauthors\tpublications\tGCC_nextclade\tGCC_usher\tGCC_assigned_2023-11" \ > rsv$aOrB.$today.metadata.tsv join -t$'\t' -o 1.2,2.1,2.6,2.4,2.5,2.8,2.9,2.10,2.11,2.13,2.14,2.15 \ <(sort renaming.tsv) \ <(sort $rsvNcbiDir/metadata.tsv \ | perl -F'/\t/' -walne '$F[3] =~ s/(: ?|$)/\t/; print join("\t", @F);') \ | sort \ | join -t$'\t' - <(join -a 1 -o 1.2,2.2 -t$'\t' renaming.tsv accToCClade | sort) \ | join -t$'\t' - <(sort sample-clades.$aOrB | sed -re 's/None/Unassigned/g') \ | join -t$'\t' - <(join -a 1 -o 1.2,2.2 -t$'\t' \ <(sed -re 's/\.[0-9]+\t/\t/;' renaming.tsv) \ $rsvDir/RSV${aOrB}_GCC_2023-11-06.tsv \ | sort) \ >> rsv$aOrB.$today.metadata.tsv pigz -f -p 8 rsv$aOrB.$today.metadata.tsv # Make a tree version description for hgPhyloPlace $matUtils extract -i rsv$aOrB.$today.pb -u samples.$aOrB.$today >& tmp.log sampleCountComma=$(wc -l < samples.$aOrB.$today \ | sed -re 's/([0-9]+)([0-9]{3})$/\1,\2/; s/([0-9]+)([0-9]{3},[0-9]{3})$/\1,\2/;') echo "$sampleCountComma genomes from INSDC (GenBank/ENA/DDBJ) ($today)" \ > hgPhyloPlace.description.$aOrB.txt # Make a taxonium view usher_to_taxonium --input rsv$aOrB.$today.pb \ --metadata rsv$aOrB.$today.metadata.tsv.gz \ --columns genbank_accession,country,location,date,authors,GCC_nextclade,GCC_usher,GCC_assigned_2023-11 \ --clade_types=placeholder,pango \ --genbank $gbff \ --name_internal_nodes \ --title "RSV-"$aOrB" $today tree with $sampleCountComma genomes from INSDC" \ --output rsv$aOrB.$today.taxonium.jsonl.gz \ >& usher_to_taxonium.$aOrB.log # Update links to latest protobuf and metadata in /gbdb directories nc=$(basename $gbff .gbff) dir=/gbdb/wuhCor1/hgPhyloPlaceData/rsv/$nc - mkdir -p $dir - ln -sf $(pwd)/rsv$aOrB.$today.pb $dir/rsv$aOrB.latest.pb - ln -sf $(pwd)/rsv$aOrB.$today.metadata.tsv.gz $dir/rsv$aOrB.latest.metadata.tsv.gz - ln -sf $(pwd)/hgPhyloPlace.description.$aOrB.txt $dir/rsv$aOrB.latest.version.txt + ssh hgwdev mkdir -p $dir + ssh hgwdev ln -sf $(pwd)/rsv$aOrB.$today.pb $dir/rsv$aOrB.latest.pb + ssh hgwdev ln -sf $(pwd)/rsv$aOrB.$today.metadata.tsv.gz $dir/rsv$aOrB.latest.metadata.tsv.gz + ssh hgwdev ln -sf $(pwd)/hgPhyloPlace.description.$aOrB.txt $dir/rsv$aOrB.latest.version.txt # Extract Newick and VCF for anyone who wants to download those instead of protobuf $matUtils extract -i rsv$aOrB.$today.pb \ -t rsv$aOrB.$today.nwk \ -v rsv$aOrB.$today.vcf >& tmp.log pigz -p 8 -f rsv$aOrB.$today.nwk rsv$aOrB.$today.vcf # Link to public trees download directory hierarchy read y m d < <(echo $today | sed -re 's/-/ /g') archive=$archiveRoot/$y/$m/$d mkdir -p $archive ln -f $(pwd)/rsv$aOrB.$today.{nwk,vcf,metadata.tsv,taxonium.jsonl}.gz $archive/ gzip -c rsv$aOrB.$today.pb > $archive/rsv$aOrB.$today.pb.gz ln -f $(pwd)/hgPhyloPlace.description.$aOrB.txt $archive/rsv$aOrB.$today.version.txt # Update 'latest' in $archiveRoot for f in $archive/rsv$aOrB.$today.*; do latestF=$(echo $(basename $f) | sed -re 's/'$today'/latest/') ln -f $f $archiveRoot/$latestF done # Update hgdownload-test link for archive asmDir=$(echo $asmAcc \ | sed -re 's@^(GC[AF])_([0-9]{3})([0-9]{3})([0-9]{3})\.([0-9]+)@\1/\2/\3/\4/\1_\2\3\4.\5@') - mkdir -p /data/apache/htdocs-hgdownload/hubs/$asmDir/UShER_RSV-$aOrB/$y/$m - ln -sf $archive /data/apache/htdocs-hgdownload/hubs/$asmDir/UShER_RSV-$aOrB/$y/$m + ssh hgwdev ln -sf $archiveRoot/rsv$aOrB.latest.* /data/apache/htdocs-hgdownload/hubs/$asmDir/UShER_RSV-$aOrB/ # rsync to hgdownload{1,2} hubs dir - for h in hgdownload1 hgdownload3; do - if rsync -a -L --delete /data/apache/htdocs-hgdownload/hubs/$asmDir/UShER_RSV-$aOrB/* \ + for h in hgdownload1 hgdownload2 hgdownload3; do + if ssh hgwdev rsync -a -L --delete /data/apache/htdocs-hgdownload/hubs/$asmDir/UShER_RSV-$aOrB/* \ qateam@$h:/mirrordata/hubs/$asmDir/UShER_RSV-$aOrB/; then true else echo "" echo "*** rsync to $h failed; disk full? ***" echo "" fi done done set +o pipefail grep 'Could not' annotate.*.log | cat grep skipping annotate.*.log | cat set -o pipefail cat hgPhyloPlace.description.A.txt zcat rsvA.$today.metadata.tsv.gz | tail -n+2 | cut -f 13,15 | sort | uniq -c echo "" cat hgPhyloPlace.description.B.txt zcat rsvB.$today.metadata.tsv.gz | tail -n+2 | cut -f 13,15 | sort | uniq -c echo "" echo "RSV GCC clades:" zcat rsvA.$today.metadata.tsv.gz | tail -n+2 | cut -f 14,16,17 | sort | uniq -c echo "" zcat rsvB.$today.metadata.tsv.gz | tail -n+2 | cut -f 14,16,17 | sort | uniq -c rm -f mutation-paths.txt *.pre*.pb final-tree.nh *.opt.pb *.pbintermediate*.pb nice gzip -f *.log *.tsv move_log* *.stderr samples.* sample-clades.*