9012336f7d4569de36ea47886405c770b23a1ea1
angie
  Tue Jun 3 11:15:43 2025 -0700
CNCB apparently shut down access so just use last downloaded set.

diff --git src/hg/utils/otto/sarscov2phylo/updateIdMapping.sh src/hg/utils/otto/sarscov2phylo/updateIdMapping.sh
index f0c19be7c3a..eca16101654 100755
--- src/hg/utils/otto/sarscov2phylo/updateIdMapping.sh
+++ src/hg/utils/otto/sarscov2phylo/updateIdMapping.sh
@@ -15,31 +15,31 @@
 
 nextmeta=$1
 nextfasta=$2
 
 scriptDir=$(dirname "${BASH_SOURCE[0]}")
 source $scriptDir/util.sh
 
 today=$(date +%F)
 ottoDir=/hive/data/outside/otto/sarscov2phylo
 mapScriptDir=~angie/chris_ncov
 # Should use a better location than this...
 installDir=/hive/users/angie/gisaid
 
 ncbiDir=$ottoDir/ncbi.$today
 cogUkDir=$ottoDir/cogUk.$today
-cncbDir=$ottoDir/cncb.$today
+cncbDir=$ottoDir/cncb.latest
 
 # Set up input files for Chris's scripts to map GISAID <--> public sequences
 cd $mapScriptDir
 rm -rf input/$today
 mkdir input/$today
 cd input/$today
 ln -sf $cncbDir/cncb.nonGenBank.fasta.xz .
 ln -sf $ncbiDir/genbank.fa.xz .
 ln -sf $cogUkDir/cog_all.fasta.xz .
 ln -sf $nextfasta .
 xcat $nextmeta | tail -n+2 | cut -f1,3 | uniq > seqToEpi
 
 cd $mapScriptDir
 time ./build.sh -t $today