1a144b066558c8c401c4440635f0f4aa68707806
angie
  Tue Jun 3 08:43:18 2025 -0700
Reduce threads to avoid lockup in usher-sampled and matOptimize.  Remove items with bogus dates to avoid crashing chronumental.  Specify B3.13 because there's also D1.1.  Update hgdownload2 --> hgdownload3 and tolerate hgdownload rsync failure.

diff --git src/hg/utils/otto/fluA/buildConcatTree.sh src/hg/utils/otto/fluA/buildConcatTree.sh
index 68f1fcac891..aaa5189b471 100755
--- src/hg/utils/otto/fluA/buildConcatTree.sh
+++ src/hg/utils/otto/fluA/buildConcatTree.sh
@@ -1,302 +1,317 @@
 #!/bin/bash
 source ~/.bashrc
 set -beEu -o pipefail
 
 # Concatenate the segments of sequences in the 2024 H5N1 outbreak and build a tree & metadata.
 
 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=32
+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 PP755620.1
             ;;
         2)
             echo PP755619.1
             ;;
         3)
             echo PP755618.1
             ;;
         4)
             echo PP753693.1
             ;;
         5)
             echo PP755616.1
             ;;
         6)
             echo PP753695.1
             ;;
         7)
             echo PP755614.1
             ;;
         8)
             echo PP753097.1
             ;;
         *)
             echo ERROR
             ;;
     esac
 }
 
 
 cd $fluADir/build/$today
 
 # First, for each segment, find the node of the segment tree that corresponds to the outbreak.
 
 # A/cattle/Texas/24-008749-007/2024 is basal for segments 1 (PB2), 2 (PB1), 3 (PA), 5 (NP) and 7 (M)
 for seg in 1 2 3 5 7; do
     segRef=$(grep NC_ $assemblyReport | tawk '$3 == '$seg' {print $7;}')
     $matUtils extract -i fluA.$asmAcc.$segRef.$today.pb -S sample-paths.$asmAcc.$segRef \
         >& tmp.log
     cladeNode=$(grep Texas/24-008749-007/2024 sample-paths.$asmAcc.$segRef \
         | awk '{print $NF;}' \
         | sed -re 's/:.*//;')
     grep -w $cladeNode sample-paths.$asmAcc.$segRef \
     | cut -f 1 > samples.h5n1_outbreak_2024.$seg
 done
 
 # A/cattle/New_Mexico/24-010193-003/2024 is basal for segments 4 (HA) and 6 (NA)
 for seg in 4 6; do
     segRef=$(grep NC_ $assemblyReport | tawk '$3 == '$seg' {print $7;}')
     $matUtils extract -i fluA.$asmAcc.$segRef.$today.pb -S sample-paths.$asmAcc.$segRef \
         >& tmp.log
     cladeNode=$(grep New_Mexico/24-010193-003/2024 sample-paths.$asmAcc.$segRef \
         | awk '{print $NF;}' \
         | sed -re 's/:.*//;')
     grep -w $cladeNode sample-paths.$asmAcc.$segRef \
     | cut -f 1 > samples.h5n1_outbreak_2024.$seg
 done
 
 # A/cattle/Texas/24-009110-018/2024 is basal for segment 8 (NS) - but it's not in the H5N1
 # NS tree (reassortment since original H5N1 NS, too distant to align)
 asmAcc=GCF_000851145.1
 seg=8
 segRef=NC_004906.1
 $matUtils extract -i fluA.$asmAcc.$segRef.$today.pb -S sample-paths.$asmAcc.$segRef \
         >& tmp.log
 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 \
 | cut -f 1,17 \
     > 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.$seg.fa \
     --excess-bandwidth 9 --terminal-bandwidth 100 --allowed-mismatches 4 \
     --gap-alignment-side right --min-seed-cover 0.1 \
     --output-fasta h5n1_outbreak_2024.$seg.aligned.fa \
         >& nextclade.$seg.log
 done
 
 $fluAScriptDir/joinSegments.py \
     --segments h5n1_outbreak_2024.{1,2,3,4,5,6,7,8}.aligned.fa \
     --output h5n1_outbreak_2024.aligned.fa \
     >& joinSegments.log
 
 cat $fluADir/h5n1_outbreak_2024/concat.fa h5n1_outbreak_2024.aligned.fa \
 | faToVcf -verbose=2 -includeNoAltN stdin stdout \
 | pigz -p 8 \
     > h5n1_outbreak_2024.in.vcf.gz
 
 $usher-sampled -T $threads -A -e 10 \
     -t emptyTree.nwk \
     -v h5n1_outbreak_2024.in.vcf.gz \
     -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
+# 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...
 $matUtils extract -i h5n1_outbreak_2024.pb.opt.gz \
+    --max-branch-length 65 \
+    -O -o tmp.pb.gz
+$matUtils extract -i tmp.pb.gz \
+    --max-branch-length 65 \
     -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
 # INSDC metadata (from HA segment; remove uniquifying INSDC accessions)
 grep -Fwf <(cut -d\| -f 2 samples.h5n1_outbreak_2024.4 | 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 -u \
+| sort -k1,1 -u \
     >> h5n1_outbreak_2024.metadata.tsv
 # Add Andersen lab metadata (from HA segment but remove _HA from names)
 grep _HA/ $fluADir/andersen_lab.srrNotGb.renamed.metadata.tsv \
 | cut -f 1,3-5,7- \
 | sed -re 's@_HA/@/@;' \
     >> h5n1_outbreak_2024.metadata.tsv
 wc -l h5n1_outbreak_2024.metadata.tsv
 
 # Add Bloom lab's Deep Mutational Scanning scores for HA and PB2
 tail -n+2 h5n1_outbreak_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=$(head -1 h5n1_outbreak_2024.metadata.tsv | sed -re 's/\t/\\t/g')
 set +o pipefail
 haFields=$(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_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 $fluADir/h5n1_outbreak_2024/concat.gbff \
     --name_internal_nodes \
-    --title "2024 H5N1 outbreak in USA, concatenated segments from INSDC and SRA ($today)" \
+    --title "2024 H5N1 B3.13 outbreak in USA, concatenated segments from INSDC and SRA ($today)" \
     --config_json $fluAScriptDir/concat.config.json \
     --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 \
     $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/
 # rsync to hgdownload hubs dir
-for h in hgdownload1 hgdownload2; do
-    rsync -a -L --delete $downloadsRoot/$asmDir/UShER_h5n1_outbreak_2024 \
-        qateam@$h:/mirrordata/hubs/$asmDir/
+for h in hgdownload1 hgdownload3; do
+    if 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