883a8a9699c47c71ab36838cc0ec878b1831cd0f
angie
  Sun Nov 7 10:10:26 2021 -0800
Nextstrain clades are now completely specified by nextstrain.clade-mutations.tsv; -c (--clade-names) input file is ignored, so no need to pass it in.

diff --git src/hg/utils/otto/sarscov2phylo/updateCombinedTree.sh src/hg/utils/otto/sarscov2phylo/updateCombinedTree.sh
index a374224..c643d9d 100755
--- src/hg/utils/otto/sarscov2phylo/updateCombinedTree.sh
+++ src/hg/utils/otto/sarscov2phylo/updateCombinedTree.sh
@@ -64,32 +64,30 @@
 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; GISAID, NCBI and COG-UK sequences downloaded $today; CNCB sequences downloaded $cncbDate" \
     > version.plusGisaid.txt
 sampleCountComma=$(echo $(wc -l < samples.$today) \
                    | sed -re 's/([0-9]+)([0-9]{3})$/\1,\2/; s/([0-9]+)([0-9]{3},[0-9]{3})$/\1,\2/;')
 echo "$sampleCountComma genomes from GISAID, GenBank, COG-UK and CNCB ($today); sarscov2phylo 13-11-20 tree with newer sequences added by UShER" \
     > hgPhyloPlace.plusGisaid.description.txt
 
 # Add nextclade annotations to protobuf
 if [ -s $ottoDir/$prevDate/cladeToName ]; then
     # Use yesterday's clade assignments to annotate clades on today's tree
     time $matUtils annotate -T 50 \
         -l \
         -i gisaidAndPublic.$today.masked.pb \
         -M $scriptDir/nextstrain.clade-mutations.tsv \
-        -c $ottoDir/$prevDate/cladeToName \
-        -f 0.95 \
         -D details.nextclade \
         -o gisaidAndPublic.$today.masked.nextclade.pb \
         >& annotate.nextclade
 else
     time $matUtils annotate -T 50 \
         -l \
         -i gisaidAndPublic.$today.masked.pb \
         -P ../nextstrain.clade-paths.tsv \
         -o gisaidAndPublic.$today.masked.nextclade.pb
 fi
 
 # Add pangolin lineage annotations to protobuf.
 if [ -s $ottoDir/$prevDate/lineageToName ]; then
     time $matUtils annotate -T 50 \
         -i gisaidAndPublic.$today.masked.nextclade.pb \