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
@@ -1,52 +1,56 @@
 #!/bin/bash
 source ~/.bashrc
 set -beEu -x -o pipefail
 
 #	Do not modify this script, modify the source tree copy:
 #	kent/src/hg/utils/otto/sarscov2phylo/updatePublic.sh
 
 usage() {
     echo "usage: $0 problematicSitesVcf"
 }
 
 if [ $# != 1 ]; then
   usage
   exit 1
 fi
 
 problematicSitesVcf=$1
 
 ottoDir=/hive/data/outside/otto/sarscov2phylo
 gisaidDir=/hive/users/angie/gisaid
 
 today=$(date +%F)
 scriptDir=$(dirname "${BASH_SOURCE[0]}")
 
 $scriptDir/gisaidFromChunks.sh
 
 cogUkDir=$ottoDir/cogUk.$today
 mkdir -p $cogUkDir
 cd $cogUkDir
 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 &