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/buildConcatTreeD1.1.sh src/hg/utils/otto/fluA/buildConcatTreeD1.1.sh
index 184fe05f541..af278e77860 100755
--- src/hg/utils/otto/fluA/buildConcatTreeD1.1.sh
+++ src/hg/utils/otto/fluA/buildConcatTreeD1.1.sh
@@ -1,320 +1,323 @@
 #!/bin/bash
 source ~/.bashrc
 set -beEu -o pipefail
 
 # Concatenate the segments of sequences in the 2024 H5N1 D1.1 outbreak and build a tree & metadata.
 
 # References selected from per-segment trees:
 # PB2	PQ664446.1	A/chicken/WA/24-030039-002/2024_H5N1|PQ664446.1|2024-10-11
 # PB1	PQ798039.1	A/chicken/WA/24-032809-001-original/2024_H5N1|PQ798039.1|2024-11-05
 # PA	PQ859340.1	A/chicken/LA/24-037003-001-original/2024_H5N1|PQ859340.1|2024-12-09
 # HA	PQ663857.1	A/Guineafowl/WA/24-030328-001-original/2024_H5N1|PQ663857.1|2024-10-15
 # NP	PQ585621.1	A/Washington/UW63494/2024_H5N1|PQ585621.1|2024-10-18
 # NA	PQ664459.1	A/chicken/WA/24-031352-001-original/2024_H5N1|PQ664459.1|2024-10-21
 # MP	PQ663860.1	A/Guineafowl/WA/24-030328-001-original/2024_H5N1|PQ663860.1|2024-10-15
 # NS	PQ797957.1	A/chicken/CA/24-032296-001-original/2024_H5N1|PQ797957.1|2024-10-30
 
 today=$1
 if [[ $today == "" ]]; then
     today=$(date +%F)
 fi
 
 fluADir=/hive/data/outside/otto/fluA
 fluANcbiDir=$fluADir/ncbi/ncbi.latest
 fluAScriptDir=$(dirname "${BASH_SOURCE[0]}")
 
 archiveRoot=/hive/users/angie/publicTreesFluA
 downloadsRoot=/data/apache/htdocs-hgdownload/hubs
 
 assemblyDir=/hive/data/outside/ncbi/genomes
 asmAcc=GCF_000864105.1
 asmDir=$(echo $asmAcc \
          | sed -re 's@^(GC[AF])_([0-9]{3})([0-9]{3})([0-9]{3})\.([0-9]+)@\1/\2/\3/\4/\1_\2\3\4.\5@')
 assemblyReport=$assemblyDir/$asmDir*/$asmAcc*_assembly_report.txt
 
 threads=16
 
 
 # Assembly reports have segment numbers but not names, so map like this:
 function segName {
     case $1 in
         1)
             echo PB2
             ;;
         2)
             echo PB1
             ;;
         3)
             echo PA
             ;;
         4)
             echo HA
             ;;
         5)
             echo NP
             ;;
         6)
             echo NA
             ;;
         7)
             echo MP
             ;;
         8)
             echo NS
             ;;
         *)
             echo ERROR
             ;;
     esac
 }
 
 # INSDC accession of basal sequence for each segment
 function segRefAcc {
     case $1 in
         1)
             echo PQ664446.1
             ;;
         2)
             echo PQ798039.1
             ;;
         3)
             echo PQ859340.1
             ;;
         4)
             echo PQ663857.1
             ;;
         5)
             echo PQ585621.1
             ;;
         6)
             echo PQ664459.1
             ;;
         7)
             echo PQ663860.1
             ;;
         8)
             echo PQ797957.1
             ;;
         *)
             echo ERROR
             ;;
     esac
 }
 
 
 cd $fluADir/build/$today
 
 # First, for each segment, find the node of the segment tree that corresponds to the outbreak.
 
 # H5N1 asmAcc for all segments except 8:
 for seg in 1 2 3 4 5 6 7; do
     segRef=$(grep NC_ $assemblyReport | tawk '$3 == '$seg' {print $7;}')
     if [[ ! -s sample-paths.$asmAcc.$segRef ]]; then
         $matUtils extract -i fluA.$asmAcc.$segRef.$today.pb -S sample-paths.$asmAcc.$segRef \
                   >& tmp.log
     fi
     # NOTE: for segments 1 (PB2), 2 (PB1), 3 (PA) and 4 (HA), we want to pick a node upstream of
     # the chosen segRefAcc (see ~angie/notes/25_02_07_fluA_H5N1_D1.1.txt).
     # 2025-04-18: also go one node back for segment 6 (NA) because of tree instability -- sometimes
     # branch is split.
     if (( $seg < 5 || $seg == 6)); then
         adjust="-1"
     else
         adjust=""
     fi
     cladeNode=$(grep $(segRefAcc $seg) sample-paths.$asmAcc.$segRef \
         | awk '{print $(NF'$adjust');}' \
         | sed -re 's/:.*//;')
     grep -w $cladeNode sample-paths.$asmAcc.$segRef \
     | cut -f 1 > samples.h5n1_D1.1_2024.$seg
 done
 
 # segment 8 (NS) ref is not in the H5N1 NS tree (reassortment since original H5N1 NS, too distant
 # to align, it's in the H9N2 tree
 asmAcc=GCF_000851145.1
 seg=8
 segRef=NC_004906.1
 if [[ ! -s sample-paths.$asmAcc.$segRef ]]; then
     $matUtils extract -i fluA.$asmAcc.$segRef.$today.pb -S sample-paths.$asmAcc.$segRef \
               >& tmp.log
 fi
 cladeNode=$(grep $(segRefAcc $seg) sample-paths.$asmAcc.$segRef \
     | awk '{print $NF;}' \
     | sed -re 's/:.*//;')
 grep -w $cladeNode sample-paths.$asmAcc.$segRef \
 | cut -f 1 > samples.h5n1_D1.1_2024.$seg
 
 # Use GenBank sequences found in the trees plus Andersen Lab assembled sequences.
 cat samples.h5n1_D1.1_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 2,15 \
 | tawk '{ if ($2 != "") { print $2; } else { print $1; } }' \
 | sort -u \
 | 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 $fluANcbiDir/genbank.fa.xz) stdin stdout \
     | faRenameRecords stdin renaming.tsv.gz h5n1_D1.1_2024.$seg.fa
     segName=$(segName $seg)
     set +o pipefail
     fastaNames $fluADir/andersen_lab.srrNotGb.renamed.fa \
     | grep _$segName \
     | grep -Fwf <(grep \|SRR samples.h5n1_D1.1_2024.* | cut -d\| -f 2) \
     | faSomeRecords $fluADir/andersen_lab.srrNotGb.renamed.fa stdin stdout \
     | sed -re '/^>/ s@_'$segName'/@/@;' \
           >> h5n1_D1.1_2024.$seg.fa
     set -o pipefail
     refAcc=$(segRefAcc $seg)
     nextclade run --input-ref $fluADir/h5n1_D1.1_2024/$refAcc.fa h5n1_D1.1_2024.$seg.fa \
               --excess-bandwidth 9 --terminal-bandwidth 100 --allowed-mismatches 4 \
               --gap-alignment-side right --min-seed-cover 0.1 \
               --output-fasta h5n1_D1.1_2024.$seg.aligned.fa \
               >& nextclade.$seg.log
 done
 
 $fluAScriptDir/joinSegments.py \
     --segments h5n1_D1.1_2024.{1,2,3,4,5,6,7,8}.aligned.fa \
     --output h5n1_D1.1_2024.aligned.fa \
     >& joinSegments.log
 
 cat $fluADir/h5n1_D1.1_2024/concat.fa h5n1_D1.1_2024.aligned.fa \
 | faToVcf -verbose=2 -includeNoAltN stdin stdout \
 | pigz -p 8 \
     > h5n1_D1.1_2024.in.vcf.gz
 
 $usher-sampled -T $threads -A -e 10 \
     -t emptyTree.nwk \
     -v h5n1_D1.1_2024.in.vcf.gz \
     -o h5n1_D1.1_2024.preOpt.pb.gz \
     --optimization_radius 0 --batch_size_per_process 100 \
     > usher.addNew.h5n1_D1.1_2024.log 2> usher-sampled.h5n1_D1.1_2024.stderr
 
 # Optimize:
 $matOptimize -T $threads -m 0.00000001 -M 1 -S move_log.h5n1_D1.1_2024 \
     -i h5n1_D1.1_2024.preOpt.pb.gz \
     -v h5n1_D1.1_2024.in.vcf.gz \
     -o h5n1_D1.1_2024.pb.opt.gz \
     >& matOptimize.h5n1_D1.1_2024.log
 chmod 664 h5n1_D1.1_2024.pb*
 
 # Collapse nodes and filter out extremely long branches that imply outside-of-outbreak sequences
 $matUtils extract -i h5n1_D1.1_2024.pb.opt.gz \
     --max-branch-length 65 \
     -O -o h5n1_D1.1_2024.pb.gz
 
 # Make a tree version description for hgPhyloPlace
 $matUtils extract -i h5n1_D1.1_2024.pb.gz -u samples.h5n1_D1.1_2024 \
     >& tmp.log
 awk -F\| '{if ($3 == "") { print $1; } else { print $2; }}' samples.h5n1_D1.1_2024 \
     > accs.h5n1_D1.1_2024.tsv
 sampleCountComma=$(wc -l < samples.h5n1_D1.1_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_D1.1_2024.txt
 
 # Metadata (no need to add clade because the outbreak is all D1.1)
 echo -e "strain\tdate\tcountry\tlocation\thost\tbioproject_accession\tbiosample_accession\tsra_accession\tauthors\tpublications" \
     > h5n1_D1.1_2024.metadata.tsv
 # INSDC metadata (from MP segment which has most samples; remove uniquifying INSDC accessions)
 grep -Fwf <(cut -d\| -f 2 samples.h5n1_D1.1_2024.7 | grep -v ^SRR) $fluANcbiDir/metadata.tsv \
 | grep -v 1970-01-01 \
 | sort \
 | perl -F'/\t/' -walne '$F[3] =~ s/(: ?|$)/\t/;  print join("\t", @F);' \
 | join -t$'\t' -o 1.2,2.6,2.4,2.5,2.9,2.10,2.11,2.12,2.14,2.15 \
     <(zcat renaming.tsv.gz | cut -d\| -f 1,3| sort) \
     - \
 | sort -k1,1 -u \
 | grep -Fwf samples.h5n1_D1.1_2024 \
     >> h5n1_D1.1_2024.metadata.tsv
 # Add Andersen lab metadata (from HA segment but remove _HA from names)
 grep -Fwf samples.h5n1_D1.1_2024.4 $fluADir/andersen_lab.srrNotGb.renamed.metadata.tsv \
 | cut -f 1,3-5,7- \
 | sed -re 's@_HA/@/@;' \
 | grep -Fwf samples.h5n1_D1.1_2024 \
     >> h5n1_D1.1_2024.metadata.tsv
 wc -l h5n1_D1.1_2024.metadata.tsv
 
 # Add Bloom lab's Deep Mutational Scanning scores for HA and PB2
 tail -n+2 h5n1_D1.1_2024.metadata.tsv \
 | sort \
 | join -t$'\t' -a 1 \
     -o 1.1,1.2,1.3,1.4,1.5,1.6,1.7,1.8,1.9,1.10,2.2,2.3,2.4,2.5,2.6,2.7,2.8,2.9,2.10,2.11 \
     - \
     <(zcat H5N1_HA_DMS_metadata.tsv.gz | tail -n+2 \
       | sed -re 's/\|[A-Z]{2}[0-9]{6}\.[0-9]+\|/|/; s@_HA/@/@;' | sort -u) \
 | join -t$'\t' -a 1 \
     -o 1.1,1.2,1.3,1.4,1.5,1.6,1.7,1.8,1.9,1.10,1.11,1.12,1.13,1.14,1.15,1.16,1.17,1.18,1.19,1.20,2.2,2.3 \
     - \
     <(zcat PB2_DMS_metadata.tsv.gz | tail -n+2 \
       | sed -re 's/\|[A-Z]{2}[0-9]{6}\.[0-9]+\|/|/; s@_PB2/@/@;' | sort -u) \
     > tmp
 oldFields=$(head -1 h5n1_D1.1_2024.metadata.tsv | sed -re 's/\t/\\t/g')
 set +o pipefail
 haFields=$(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_D1.1_2024.metadata.tsv
 cat tmp >> h5n1_D1.1_2024.metadata.tsv
 rm tmp
 pigz -f -p 8 h5n1_D1.1_2024.metadata.tsv
 
 usher_to_taxonium --input h5n1_D1.1_2024.pb.gz \
     --metadata h5n1_D1.1_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 $fluADir/h5n1_D1.1_2024/concat.gbff \
     --name_internal_nodes \
     --title "2024 H5N1 D1.1 outbreak in USA, concatenated segments from INSDC and SRA ($today)" \
     --config_json $fluAScriptDir/concat.config.json \
+    --overlay_html $fluAScriptDir/taxonium_overlay_d1_1.html \
     --chronumental \
     --chronumental_steps 500 \
     --chronumental_add_inferred_date chronumental_date \
     --output h5n1_D1.1_2024.jsonl.gz \
     >& utt.log
 
 # Link to /gbdb/ location
 dir=/gbdb/wuhCor1/hgPhyloPlaceData/influenzaA/h5n1_D1.1_2024
-mkdir -p $dir
-ln -sf $(pwd)/h5n1_D1.1_2024.pb.gz $dir/h5n1_D1.1_2024.latest.pb.gz
-ln -sf $(pwd)/h5n1_D1.1_2024.metadata.tsv.gz $dir/h5n1_D1.1_2024.latest.metadata.tsv.gz
-ln -sf $(pwd)/hgPhyloPlace.description.h5n1_D1.1_2024.txt \
+ssh hgwdev mkdir -p $dir
+ssh hgwdev ln -sf $(pwd)/h5n1_D1.1_2024.pb.gz $dir/h5n1_D1.1_2024.latest.pb.gz
+ssh hgwdev ln -sf $(pwd)/h5n1_D1.1_2024.metadata.tsv.gz $dir/h5n1_D1.1_2024.latest.metadata.tsv.gz
+ssh hgwdev ln -sf $(pwd)/hgPhyloPlace.description.h5n1_D1.1_2024.txt \
     $dir/h5n1_D1.1_2024.latest.version.txt
 
 # Extract Newick and VCF for anyone who wants to download those instead of protobuf
 $matUtils extract -i h5n1_D1.1_2024.pb.gz \
     -t h5n1_D1.1_2024.nwk \
     -v h5n1_D1.1_2024.vcf >& tmp.log
 pigz -p 8 -f h5n1_D1.1_2024.nwk h5n1_D1.1_2024.vcf
 
 # Make a ref + all fasta download file for Delphy folks
 cat $fluADir/h5n1_D1.1_2024/concat.fa h5n1_D1.1_2024.aligned.fa \
 | pigz -p 8 \
     > h5n1_D1.1_2024.msa.fa.gz
 
 # Update 'latest' in $archiveRoot
 for e in jsonl.gz metadata.tsv.gz nwk.gz pb.gz vcf.gz msa.fa.gz ; do
     ln -sf $(pwd)/h5n1_D1.1_2024.$e $archiveRoot/h5n1_D1.1_2024.latest.$e
 done
 ln -sf $(pwd)/hgPhyloPlace.description.h5n1_D1.1_2024.txt \
     $archiveRoot/h5n1_D1.1_2024.latest.version.txt
 
 # Update hgdownload-test link for archive (adding assembly/segRef hierarchy)
-mkdir -p $downloadsRoot/$asmDir/UShER_h5n1_D1.1_2024
-ln -sf $archiveRoot/h5n1_D1.1_2024.latest.* $downloadsRoot/$asmDir/UShER_h5n1_D1.1_2024/
+ssh hgwdev mkdir -p $downloadsRoot/$asmDir/UShER_h5n1_D1.1_2024
+ssh hgwdev ln -sf $archiveRoot/h5n1_D1.1_2024.latest.* $downloadsRoot/$asmDir/UShER_h5n1_D1.1_2024/
 # rsync to hgdownload hubs dir
-for h in hgdownload1 hgdownload3; do
-    if rsync -a -L --delete $downloadsRoot/$asmDir/UShER_h5n1_D1.1_2024 \
+for h in hgdownload1 hgdownload2 hgdownload3; do
+    if ssh hgwdev rsync -a -L --delete $downloadsRoot/$asmDir/UShER_h5n1_D1.1_2024 \
              qateam@$h:/mirrordata/hubs/$asmDir/ ; then
         true
     else
         echo ""
         echo "*** rsync to $h failed -- disk full ? ***"
         echo ""
     fi
 done