be4311c07e14feb728abc6425ee606ffaa611a58
markd
  Fri Jan 22 06:46:58 2021 -0800
merge with master

diff --git src/hg/utils/otto/sarscov2phylo/getCogUk.sh src/hg/utils/otto/sarscov2phylo/getCogUk.sh
index d2a2e2c..ab711c7 100755
--- src/hg/utils/otto/sarscov2phylo/getCogUk.sh
+++ src/hg/utils/otto/sarscov2phylo/getCogUk.sh
@@ -1,27 +1,27 @@
 #!/bin/bash
 
-set -beEu -o pipefail
+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
 
 wget -q $cogUrlBase/cog_all.fasta
 wget -q $cogUrlBase/cog_metadata.csv
 
 xz -f -T 50 cog_all.fasta
 
 tail -n +2 cog_metadata.csv \
 | awk -F, '{print $1 "\t" $4;}' | sort > cogUkToDate
 
 rm -f $ottoDir/cogUk.latest
 ln -s cogUk.$today $ottoDir/cogUk.latest