ed655b70beb98c16d99689a1485b511d0b27d408
angie
  Tue Jun 3 11:20:34 2025 -0700
Tolerate updateIdMapping.sh failure (always caused by download failure) and let build proceed with latest available mapping.

diff --git src/hg/utils/otto/sarscov2phylo/updatePublic.sh src/hg/utils/otto/sarscov2phylo/updatePublic.sh
index 446dbf58caa..529eee0474c 100755
--- src/hg/utils/otto/sarscov2phylo/updatePublic.sh
+++ src/hg/utils/otto/sarscov2phylo/updatePublic.sh
@@ -27,32 +27,35 @@
 
 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 &
 
 cncbDir=$ottoDir/cncb.$today
 mkdir -p $cncbDir
 cd $cncbDir && time $scriptDir/getCncb.sh >& getCncb.log &
 
 wait
 
-time $scriptDir/updateIdMapping.sh \
-    $gisaidDir/{metadata_batch_$today.tsv.gz,sequences_batch_$today.fa.xz}
+if ! time $scriptDir/updateIdMapping.sh \
+              $gisaidDir/{metadata_batch_$today.tsv.gz,sequences_batch_$today.fa.xz} ; then
+    echo "*** updateIdMapping failed -- proceeding with .latest versions:"
+    ls -l $epiToPublic $ottoDir/ncbi.latest $ottoDir/cogUk.latest $ottoDir/cncb.latest
+fi
 
 buildDir=$ottoDir/$today
 mkdir -p $buildDir
 cd $buildDir
 
 time $scriptDir/updateCombinedTree.sh $prevDate $today $problematicSitesVcf \
     >& updateCombinedTree.log
 
 echo ""
 cat hgPhyloPlace.description.txt
 cat hgPhyloPlace.plusGisaid.description.txt
 
 set +o pipefail
 grep skip annotate.pango annotate.nextclade | cat
 grep 'Could not' annotate.pango annotate.nextclade | cat