41b65f6c5dd2d79bf2d959abfa8bfa82529d649b
angie
  Mon Nov 29 15:57:11 2021 -0800
After completion, grep for signs of trouble when annotating clades & lineages.

diff --git src/hg/utils/otto/sarscov2phylo/updatePublic.sh src/hg/utils/otto/sarscov2phylo/updatePublic.sh
index 20b9ed6..6e286c9 100755
--- src/hg/utils/otto/sarscov2phylo/updatePublic.sh
+++ src/hg/utils/otto/sarscov2phylo/updatePublic.sh
@@ -30,23 +30,27 @@
 time $scriptDir/getCogUk.sh >& getCogUk.log
 
 ncbiDir=$ottoDir/ncbi.$today
 mkdir -p $ncbiDir
 cd $ncbiDir
 time $scriptDir/getNcbi.sh >& getNcbi.log
 
 time $scriptDir/updateIdMapping.sh \
     $gisaidDir/{metadata_batch_$today.tsv.gz,sequences_batch_$today.fa.xz}
 
 buildDir=$ottoDir/$today
 mkdir -p $buildDir
 cd $buildDir
 
 prevDate=$(date -d yesterday +%F)
-time $scriptDir/updateCombinedTree.sh $prevDate $today $problematicSitesVcf >& updateCombinedTree.log
+time $scriptDir/updateCombinedTree.sh $prevDate $today $problematicSitesVcf \
+    >& updateCombinedTree.log
 
 echo ""
 cat hgPhyloPlace.description.txt
 cat hgPhyloPlace.plusGisaid.description.txt
 
+grep skip annotate.pango annotate.nextclade
+grep 'Could not' annotate.pango annotate.nextclade
+
 # Clean up
 nice xz -f new*fa &