0b01886bcc0f6e4f6019edc35f03052b7aa49156
angie
  Sun Feb 26 11:06:33 2023 -0800
Send verbose taxonium output to separate log file

diff --git src/hg/utils/otto/sarscov2phylo/updateCombinedTree.sh src/hg/utils/otto/sarscov2phylo/updateCombinedTree.sh
index 314cd60..c7d3410 100755
--- src/hg/utils/otto/sarscov2phylo/updateCombinedTree.sh
+++ src/hg/utils/otto/sarscov2phylo/updateCombinedTree.sh
@@ -162,21 +162,22 @@
     ln -sf `pwd`/gisaidAndPublic.$today.metadata.tsv.gz \
         $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 $dir/
     ln -sf `pwd`/samples.$today.gz $dir/public.plusGisaid.names.gz
 done
 
 # 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
+    --output gisaidAndPublic.$today.masked.taxonium.jsonl.gz \
+    >& utt.log
 
 $scriptDir/extractPublicTree.sh $today $prevDate
 
 set +o pipefail
 grep skipping annotate* | cat