5dd7dc49abd77ba2cbbebba8d818cdacf5d00af8
angie
  Thu Jun 22 10:17:00 2023 -0700
pangoLEARN has been discontinued so use default usher mode in pangolin and skip scorpio for speed.

diff --git src/hg/utils/otto/sarscov2phylo/runPangolin.sh src/hg/utils/otto/sarscov2phylo/runPangolin.sh
index 63786a5..82a25ef 100755
--- src/hg/utils/otto/sarscov2phylo/runPangolin.sh
+++ src/hg/utils/otto/sarscov2phylo/runPangolin.sh
@@ -1,16 +1,16 @@
 #!/bin/bash
 source ~/.bashrc
 conda activate pangolin
 set -beEu -x -o pipefail
 
 # Run pangolin/pangoLEARN on a file (not pipe) and output full CSV
 # (suitable for cluster run on faSplit sequence chunks)
 
 fa=$1
 out=$fa.pangolin.csv
 
 threadCount=6
 
 logfile=$(mktemp)
-pangolin -t $threadCount --analysis-mode pangolearn $fa --outfile $out > $logfile 2>&1
+pangolin -t $threadCount --skip-scorpio $fa --outfile $out > $logfile 2>&1
 rm $logfile