724c2bc191aa30074eb93775ede264f38058d6bc
angie
  Wed Sep 22 17:53:14 2021 -0700
Always use -f (so reruns don't fail).

diff --git src/hg/utils/otto/sarscov2phylo/updateCombinedTree.sh src/hg/utils/otto/sarscov2phylo/updateCombinedTree.sh
index f867a2c..55347b0 100755
--- src/hg/utils/otto/sarscov2phylo/updateCombinedTree.sh
+++ src/hg/utils/otto/sarscov2phylo/updateCombinedTree.sh
@@ -401,31 +401,31 @@
 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 \
         -c $ottoDir/$prevDate/cladeToName \
         -f 0.95 \
         -D details.nextclade \
         -o gisaidAndPublic.$today.masked.nextclade.pb \
-        >& annnotate.nextclade
+        >& 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 \
         -c $ottoDir/$prevDate/lineageToName \
         -f 0.95 \
         -D details.pango \
@@ -476,18 +476,18 @@
         $dir/public.plusGisaid.latest.metadata.tsv.gz
     ln -sf `pwd`/hgPhyloPlace.plusGisaid.description.txt $dir/public.plusGisaid.latest.version.txt
     ln -sf `pwd`/epiToPublic.latest $dir/
 done
 
 # Make Taxodium-formatted protobuf for display
 zcat /hive/data/genomes/wuhCor1/goldenPath/bigZips/genes/ncbiGenes.gtf.gz > ncbiGenes.gtf
 zcat /hive/data/genomes/wuhCor1/wuhCor1.fa.gz > wuhCor1.fa
 zcat gisaidAndPublic.$today.metadata.tsv.gz > metadata.tmp.tsv
 time $matUtils extract -i gisaidAndPublic.$today.masked.pb \
     -f wuhCor1.fa \
     -g ncbiGenes.gtf \
     -M metadata.tmp.tsv \
     --write-taxodium gisaidAndPublic.$today.masked.taxodium.pb
 rm metadata.tmp.tsv wuhCor1.fa
-gzip gisaidAndPublic.$today.masked.taxodium.pb
+gzip -f gisaidAndPublic.$today.masked.taxodium.pb
 
 $scriptDir/extractPublicTree.sh $today