4a51b1bbc3d9b23dd5a36e4712250ec89f009c2c
angie
  Fri Aug 26 11:44:17 2022 -0700
Updating usage for pangolin v4.

diff --git src/hg/utils/otto/sarscov2phylo/runPangolin.sh src/hg/utils/otto/sarscov2phylo/runPangolin.sh
index 836ce41..9488261 100755
--- src/hg/utils/otto/sarscov2phylo/runPangolin.sh
+++ src/hg/utils/otto/sarscov2phylo/runPangolin.sh
@@ -1,10 +1,13 @@
 #!/bin/bash
 source ~/.bashrc
 conda activate pangolin
-set -beEu -o pipefail
+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
 logfile=$(mktemp)
-pangolin $fa --outfile $out > $logfile 2>&1
+pangolin --analysis-mode pangolearn $fa --outfile $out > $logfile 2>&1
 rm $logfile