0b3aed10ba50cdda1d27a4b3cb170fbde09b6060
angie
  Thu Jun 6 10:55:24 2024 -0700
Minor: move compression of new*.fa files into updateCombinedTree.sh to make manual copy-paste run completion a little easier.

diff --git src/hg/utils/otto/sarscov2phylo/updateCombinedTree.sh src/hg/utils/otto/sarscov2phylo/updateCombinedTree.sh
index def7a41..1377c77 100755
--- src/hg/utils/otto/sarscov2phylo/updateCombinedTree.sh
+++ src/hg/utils/otto/sarscov2phylo/updateCombinedTree.sh
@@ -198,15 +198,18 @@
 # Make Taxonium v2 protobuf for display
 usher_to_taxonium --input gisaidAndPublic.$today.masked.pb \
     --metadata gisaidAndPublic.$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 \
     --title "$today tree with sequences from GISAID, INSDC, COG-UK and CNCB" \
     --output gisaidAndPublic.$today.masked.taxonium.jsonl.gz \
     >& utt.log &
 
 $scriptDir/extractPublicTree.sh $today $prevDate
 
 set +o pipefail
 grep skipping annotate* | cat
+
+# Clean up
+nice xz -f new*fa &