edc4389658f330657da35d00e56837afdc95c4a7
angie
  Mon Jan 9 18:02:05 2023 -0800
Use as many threads as possible on the ku nodes, with current memory requirements.

diff --git src/hg/utils/otto/sarscov2phylo/runPangolin.sh src/hg/utils/otto/sarscov2phylo/runPangolin.sh
index b10947c..63786a5 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=5
+threadCount=6
 
 logfile=$(mktemp)
 pangolin -t $threadCount --analysis-mode pangolearn $fa --outfile $out > $logfile 2>&1
 rm $logfile