f1b5392d9fb6337cf2e2f9d55484a2950ebb3b37
angie
  Tue Nov 14 17:10:21 2023 -0800
CNCB is now updating daily.

diff --git src/hg/utils/otto/sarscov2phylo/updateIdMapping.sh src/hg/utils/otto/sarscov2phylo/updateIdMapping.sh
index 69f2a00..f0c19be 100755
--- src/hg/utils/otto/sarscov2phylo/updateIdMapping.sh
+++ src/hg/utils/otto/sarscov2phylo/updateIdMapping.sh
@@ -15,32 +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
-# Last time I checked, CNCB had not updated since September, just keep using what we have
-cncbDir=$ottoDir/cncb.latest
+cncbDir=$ottoDir/cncb.$today
 
 # 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