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/extractPublicTree.sh src/hg/utils/otto/sarscov2phylo/extractPublicTree.sh
index b1fdda1..dd6e7e7 100755
--- src/hg/utils/otto/sarscov2phylo/extractPublicTree.sh
+++ src/hg/utils/otto/sarscov2phylo/extractPublicTree.sh
@@ -96,31 +96,31 @@
 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 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 public-$today.metadata.tsv.gz > metadata.tmp.tsv
 time $matUtils extract -i public-$today.all.masked.pb \
     -f wuhCor1.fa \
     -g ncbiGenes.gtf \
     -M metadata.tmp.tsv \
     --write-taxodium public-$today.all.masked.taxodium.pb
 rm metadata.tmp.tsv wuhCor1.fa
-gzip public-$today.all.masked.taxodium.pb
+gzip -f public-$today.all.masked.taxodium.pb
 
 # Link to public trees download directory hierarchy
 archiveRoot=/hive/users/angie/publicTrees
 read y m d < <(echo $today | sed -re 's/-/ /g')
 archive=$archiveRoot/$y/$m/$d
 mkdir -p $archive
 gzip -c public-$today.all.nwk > $archive/public-$today.all.nwk.gz
 ln -f `pwd`/public-$today.all.masked.{pb,vcf.gz} $archive/
 gzip -c public-$today.all.masked.pb > $archive/public-$today.all.masked.pb.gz
 ln -f `pwd`/public-$today.metadata.tsv.gz $archive/
 gzip -c public-$today.all.masked.nextclade.pangolin.pb \
     > $archive/public-$today.all.masked.nextclade.pangolin.pb.gz
 if [ -s lineageToPublicName ]; then
     gzip -c lineageToPublicName > $archive/lineageToPublicName.tsv.gz
 else