7f46acdf8f879de28c3ba40534e58a881941e168
angie
  Sun Feb 4 09:24:53 2024 -0800
CNCB is updated daily so make version.txt more concise.

diff --git src/hg/utils/otto/sarscov2phylo/extractPublicTree.sh src/hg/utils/otto/sarscov2phylo/extractPublicTree.sh
index 6ebf17f..29b1d0c 100755
--- src/hg/utils/otto/sarscov2phylo/extractPublicTree.sh
+++ src/hg/utils/otto/sarscov2phylo/extractPublicTree.sh
@@ -74,32 +74,31 @@
     > public-$today.metadata.tsv.gz
 
 rm public-$today.all.masked.pb
 ln -f public-$today.all.masked.nextclade.pangolin.pb public-$today.all.masked.pb
 
 # Save paths for use tomorrow.
 $matUtils extract -i public-$today.all.masked.pb -C clade-paths.public
 tail -n+2 clade-paths.public \
 | grep -E '^[12]' \
 | cut -f 1,3 > cladeToPath.public
 tail -n+2 clade-paths.public \
 | grep -E '^[A-Za-z]' \
 | cut -f 1,3 > lineageToPath.public
 
 
-cncbDate=$(ls -l $cncbDir | sed -re 's/.*cncb\.([0-9]{4}-[0-9][0-9]-[0-9][0-9]).*/\1/')
-echo "sarscov2phylo release 13-11-20; NCBI and COG-UK sequences downloaded $today; CNCB sequences downloaded $cncbDate" \
+echo "sarscov2phylo release 13-11-20; NCBI, COG-UK and CNCB sequences downloaded $today" \
     > version.txt
 
 $matUtils extract -i public-$today.all.masked.pb -u samples.public.$today
 sampleCountComma=$(echo $(wc -l < samples.public.$today) \
                    | sed -re 's/([0-9]+)([0-9]{3})$/\1,\2/; s/([0-9]+)([0-9]{3},[0-9]{3})$/\1,\2/;')
 echo "$sampleCountComma genomes from GenBank, COG-UK and CNCB ($today); sarscov2phylo 13-11-20 tree with newer sequences added by UShER" \
     > hgPhyloPlace.description.txt
 
 # Make Taxonium V2 .jsonl.gz protobuf for display
 usher_to_taxonium --input public-$today.all.masked.pb \
     --metadata public-$today.metadata.tsv.gz \
     --genbank ~angie/github/taxonium/taxoniumtools/test_data/hu1.gb \
     --columns genbank_accession,country,date,pangolin_lineage,pango_lineage_usher \
     --clade_types=nextstrain,pango \
     --name_internal_nodes \