0b0ce9ae275e9f648f37535a0fe627fccdf6807e
angie
  Fri Feb 26 14:30:47 2021 -0800
COG-UK metadata columns changed again.

diff --git src/hg/utils/otto/sarscov2phylo/getCogUk.sh src/hg/utils/otto/sarscov2phylo/getCogUk.sh
index f17146f..9fb1243 100755
--- src/hg/utils/otto/sarscov2phylo/getCogUk.sh
+++ src/hg/utils/otto/sarscov2phylo/getCogUk.sh
@@ -1,26 +1,26 @@
 #!/bin/bash
 
 set -beEux -o pipefail
 
 # Download latest COG-UK fasta and metadata; update $ottoDir/cogUk.latest link.
 
 scriptDir=$(dirname "${BASH_SOURCE[0]}")
 source $scriptDir/util.sh
 
 today=$(date +%F)
 
 ottoDir=/hive/data/outside/otto/sarscov2phylo
 cogUrlBase=https://cog-uk.s3.climb.ac.uk/phylogenetics/latest
 
 mkdir -p $ottoDir/cogUk.$today
 cd $ottoDir/cogUk.$today
 
 curl -S -s $cogUrlBase/cog_all.fasta | xz -T 50 > cog_all.fasta.xz
 curl -S -s $cogUrlBase/cog_metadata.csv > cog_metadata.csv
 curl -S -s $cogUrlBase/cog_global_tree.newick > cog_global_tree.newick
 
 tail -n +2 cog_metadata.csv \
-| awk -F, '{print $1 "\t" $4;}' | sort > cogUkToDate
+| awk -F, '{print $1 "\t" $5;}' | sort > cogUkToDate
 
 rm -f $ottoDir/cogUk.latest
 ln -s cogUk.$today $ottoDir/cogUk.latest