6199485d849f1a1ecce4ce6f57fa01d4eb6097dd
angie
  Mon Jul 10 12:02:57 2023 -0700
No more pangolearn mode.

diff --git src/hg/utils/otto/sarscov2phylo/getCncb.sh src/hg/utils/otto/sarscov2phylo/getCncb.sh
index abf4910..56689ec 100755
--- src/hg/utils/otto/sarscov2phylo/getCncb.sh
+++ src/hg/utils/otto/sarscov2phylo/getCncb.sh
@@ -105,27 +105,27 @@
         --output-tsv nextclade.new.full.tsv.gz  >& nextclade.log
     zcat nextclade.new.full.tsv.gz | cut -f 1,2 | tail -n+2 >> nextclade.tsv
     sort -u nextclade.tsv > tmp
     mv tmp nextclade.tsv
     cat nextclade.new.full.tsv.gz >> nextclade.full.tsv.gz
 fi
 
 # Run pangolin
 cp ../cncb.latest/pangolin.tsv .
 if [ -s new.accs.fa ]; then
     set +x
     . ~/.bashrc
     conda activate pangolin
     set -x
     set -e
-    time pangolin -t 20 new.accs.fa --analysis-mode pangolearn --outfile lineages.csv \
+    time pangolin -t 20 new.accs.fa --skip-scorpio --outfile lineages.csv \
         >& pangolin.log
     awk -F, '{print $1 "\t" $2;}' lineages.csv | tail -n+2 >> pangolin.tsv
     sort -u pangolin.tsv > tmp
     mv tmp pangolin.tsv
     conda deactivate
 fi
 
 rm new.accs.fa
 
 rm -f $ottoDir/cncb.latest
 ln -s cncb.$today $ottoDir/cncb.latest