8d5f0115cf9ab2b99f18a1467c0be02a6ae55de4
angie
  Thu Jun 18 15:18:03 2026 -0700
Use taxonium overlay html to describe the trees.  Adjust filters.  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/fluA/buildConcatTree.sh src/hg/utils/otto/fluA/buildConcatTree.sh
index aaa5189b471..2991c28d12f 100755
--- src/hg/utils/otto/fluA/buildConcatTree.sh
+++ src/hg/utils/otto/fluA/buildConcatTree.sh
@@ -130,31 +130,33 @@
 cladeNode=$(grep Texas/24-009110-018/2024 sample-paths.$asmAcc.$segRef \
     | awk '{print $NF;}' \
     | sed -re 's/:.*//;')
 grep -w $cladeNode sample-paths.$asmAcc.$segRef \
 | cut -f 1 > samples.h5n1_outbreak_2024.$seg
 
 # Use GenBank sequences found in the trees plus all Andersen Lab assembled sequences.
 # Exclude some sequences that would require the root to be further back than my selected segments.
 cat samples.h5n1_outbreak_2024.* | grep -v \|SRR | cut -d\| -f 2 \
 | grep -Fwf - $fluANcbiDir/metadata.tsv \
 | grep -v 1969-12-31 \
 | grep -v 1970-01-01 \
 | cut -f 15 | sort -u \
 | grep -vE 'A/Texas/37/2024|24-003692-001|24-005915-001|23-038138-001|24-006483-001' \
 | grep -Ff - $fluANcbiDir/metadata.tsv \
+| grep -vE ' clone ?[0-9]+' \
 | cut -f 1,17 \
+| grep -Fwf <(zcat renaming.tsv.gz | cut -f 1) \
     > cladeAccToSeg
 # Extract the sequences into per-segment fasta files... renamed from accession to tree name.
 # joinSegments.py below will ignore the uniquifying INSDC accession part of names.  Remove the
 # uniquifying segment name from Andersen Lab sequences.
 for seg in 1 2 3 4 5 6 7 8; do
     tawk '$2 == '$seg' {print $1;}' cladeAccToSeg \
     | faSomeRecords <(xzcat $fluANcbiDir/genbank.fa.xz) stdin stdout \
     | faRenameRecords stdin renaming.tsv.gz h5n1_outbreak_2024.$seg.fa
     segName=$(segName $seg)
     fastaNames $fluADir/andersen_lab.srrNotGb.renamed.fa | grep _$segName/ \
     | faSomeRecords $fluADir/andersen_lab.srrNotGb.renamed.fa stdin stdout \
     | sed -re '/^>/ s@_'$segName'/@/@;' \
         >> h5n1_outbreak_2024.$seg.fa
     refAcc=$(segRefAcc $seg)
     nextclade run --input-ref $fluADir/h5n1_outbreak_2024/$refAcc.fa h5n1_outbreak_2024.$seg.fa \
@@ -180,34 +182,34 @@
     -o h5n1_outbreak_2024.preOpt.pb.gz \
     --optimization_radius 0 --batch_size_per_process 100 \
     > usher.addNew.h5n1_outbreak_2024.log 2> usher-sampled.h5n1_outbreak_2024.stderr
 
 # Optimize:
 $matOptimize -T $threads -m 0.00000001 -M 1 -S move_log.h5n1_outbreak_2024 \
     -i h5n1_outbreak_2024.preOpt.pb.gz \
     -o h5n1_outbreak_2024.pb.opt.gz \
     >& matOptimize.h5n1_outbreak_2024.log
 chmod 664 h5n1_outbreak_2024.pb*
 
 # Collapse nodes and filter out extremely long branches that imply outside-of-outbreak sequences
 # Sometimes that filtering needs to be done twice!  I guess getting rid of some long branches
 # can create others.  I hope we don't need more than two rounds...
 $matUtils extract -i h5n1_outbreak_2024.pb.opt.gz \
-    --max-branch-length 65 \
+    --max-branch-length 50 \
     -O -o tmp.pb.gz
 $matUtils extract -i tmp.pb.gz \
-    --max-branch-length 65 \
+    --max-branch-length 50 \
     -O -o h5n1_outbreak_2024.pb.gz
 
 # Make a tree version description for hgPhyloPlace
 $matUtils extract -i h5n1_outbreak_2024.pb.gz -u samples.h5n1_outbreak_2024 \
     >& tmp.log
 awk -F\| '{if ($3 == "") { print $1; } else { print $2; }}' samples.h5n1_outbreak_2024 \
     > accs.h5n1_outbreak_2024.tsv
 sampleCountComma=$(wc -l < samples.h5n1_outbreak_2024 \
     | sed -re 's/([0-9]+)([0-9]{3})$/\1,\2/; s/([0-9]+)([0-9]{3},[0-9]{3})$/\1,\2/;')
 echo "$sampleCountComma genomes from INSDC (GenBank/ENA/DDBJ) or SRA ($today)" \
     > hgPhyloPlace.description.h5n1_outbreak_2024.txt
 
 # Metadata (no need to add clade because the outbreak is all B3.13)
 echo -e "strain\tdate\tcountry\tlocation\thost\tbioproject_accession\tbiosample_accession\tsra_accession\tauthors\tpublications" \
     > h5n1_outbreak_2024.metadata.tsv
@@ -247,71 +249,70 @@
 haFields=$(zcat H5N1_HA_DMS_metadata.tsv.gz | cut -f 2- | head -1 | sed -re 's/\t/\\t/g')
 pb2Fields=$(zcat PB2_DMS_metadata.tsv.gz | cut -f 2-3 | head -1 | sed -re 's/\t/\\t/g')
 set -o pipefail
 echo -e "$oldFields\t$haFields\t$pb2Fields" > h5n1_outbreak_2024.metadata.tsv
 cat tmp >> h5n1_outbreak_2024.metadata.tsv
 rm tmp
 pigz -f -p 8 h5n1_outbreak_2024.metadata.tsv
 
 usher_to_taxonium --input h5n1_outbreak_2024.pb.gz \
     --metadata h5n1_outbreak_2024.metadata.tsv.gz \
     --columns host,country,location,date,authors,mouse_escape,ferret_escape,cell_entry,stability,sa26_increase,mouse_escape_mutations,ferret_escape_mutations,cell_entry_mutations,stability_mutations,sa26_increase_mutations,mutdiffsel,mutdiffsel_mutations \
     --genbank $fluADir/h5n1_outbreak_2024/concat.gbff \
     --name_internal_nodes \
     --title "2024 H5N1 B3.13 outbreak in USA, concatenated segments from INSDC and SRA ($today)" \
     --config_json $fluAScriptDir/concat.config.json \
+    --overlay_html $fluAScriptDir/taxonium_overlay_b3_13.html \
     --chronumental \
     --chronumental_steps 500 \
     --chronumental_add_inferred_date chronumental_date \
     --output h5n1_outbreak_2024.jsonl.gz \
     >& utt.log
 
 # Link to /gbdb/ location
 dir=/gbdb/wuhCor1/hgPhyloPlaceData/influenzaA/h5n1_outbreak_2024
-mkdir -p $dir
-ln -sf $(pwd)/h5n1_outbreak_2024.pb.gz $dir/h5n1_outbreak_2024.latest.pb.gz
-ln -sf $(pwd)/h5n1_outbreak_2024.metadata.tsv.gz $dir/h5n1_outbreak_2024.latest.metadata.tsv.gz
-ln -sf $(pwd)/hgPhyloPlace.description.h5n1_outbreak_2024.txt \
+ssh hgwdev mkdir -p $dir
+ssh hgwdev ln -sf $(pwd)/h5n1_outbreak_2024.pb.gz $dir/h5n1_outbreak_2024.latest.pb.gz
+ssh hgwdev ln -sf $(pwd)/h5n1_outbreak_2024.metadata.tsv.gz $dir/h5n1_outbreak_2024.latest.metadata.tsv.gz
+ssh hgwdev ln -sf $(pwd)/hgPhyloPlace.description.h5n1_outbreak_2024.txt \
     $dir/h5n1_outbreak_2024.latest.version.txt
 
 # Extract Newick and VCF for anyone who wants to download those instead of protobuf
 $matUtils extract -i h5n1_outbreak_2024.pb.gz \
     -t h5n1_outbreak_2024.nwk \
     -v h5n1_outbreak_2024.vcf >& tmp.log
 pigz -p 8 -f h5n1_outbreak_2024.nwk h5n1_outbreak_2024.vcf
 
 # Make a ref + all fasta download file for Delphy folks
 cat $fluADir/h5n1_outbreak_2024/concat.fa h5n1_outbreak_2024.aligned.fa \
 | pigz -p 8 \
     > h5n1_outbreak_2024.msa.fa.gz
 
 # Link to public trees archive directory (no assembly/segRef hierarchy, just by date)
 read y m d < <(echo $today | sed -re 's/-/ /g')
 archive=$archiveRoot/$y/$m/$d
 mkdir -p $archive
 ln -f $(pwd)/h5n1_outbreak_2024.{nwk,vcf,pb,metadata.tsv,msa.fa}.gz $archive/
 if [ -s h5n1_outbreak_2024.jsonl.gz ]; then
     ln -f $(pwd)/h5n1_outbreak_2024.jsonl.gz $archive/
 fi
 ln -f $(pwd)/hgPhyloPlace.description.h5n1_outbreak_2024.txt \
     $archive/h5n1_outbreak_2024.version.txt
 
 # Update 'latest' in $archiveRoot
 for e in jsonl.gz metadata.tsv.gz nwk.gz pb.gz vcf.gz version.txt msa.fa.gz ; do
     ln -f $archive/h5n1_outbreak_2024.$e $archiveRoot/h5n1_outbreak_2024.latest.$e
 done
 
 # Update hgdownload-test link for archive (adding assembly/segRef hierarchy)
-mkdir -p $downloadsRoot/$asmDir/UShER_h5n1_outbreak_2024/$y/$m/$d
-ln -sf $archive/h5n1_outbreak_2024.* $downloadsRoot/$asmDir/UShER_h5n1_outbreak_2024/$y/$m/$d/
-ln -sf $archiveRoot/h5n1_outbreak_2024.latest.* $downloadsRoot/$asmDir/UShER_h5n1_outbreak_2024/
+ssh hgwdev ln -sf $archiveRoot/h5n1_outbreak_2024.latest.* $downloadsRoot/$asmDir/UShER_h5n1_outbreak_2024/
 # rsync to hgdownload hubs dir
-for h in hgdownload1 hgdownload3; do
-    if rsync -a -L --delete $downloadsRoot/$asmDir/UShER_h5n1_outbreak_2024 \
+for h in hgdownload1 hgdownload2 hgdownload3; do
+    if ssh hgwdev rsync -a -L --delete $downloadsRoot/$asmDir/UShER_h5n1_outbreak_2024 \
              qateam@$h:/mirrordata/hubs/$asmDir/ ; then
         true
     else
         echo ""
         echo "*** rsync to $h failed -- disk full ? ***"
         echo ""
     fi
 done