ba4425b7d509f2d52bec87b22c3cd8a6802ef3db
angie
  Thu Jun 22 10:17:25 2023 -0700
Not making full nextalign.fa.xz at this point, just incrementals.

diff --git src/hg/utils/otto/sarscov2phylo/getCncb.sh src/hg/utils/otto/sarscov2phylo/getCncb.sh
index 49dba58..abf4910 100755
--- src/hg/utils/otto/sarscov2phylo/getCncb.sh
+++ src/hg/utils/otto/sarscov2phylo/getCncb.sh
@@ -89,31 +89,31 @@
 cat <(xzcat ../cncb.latest/cncb.nonGenBank.acc.fasta.xz) new.accs.fa \
 | xz -T 20 > cncb.nonGenBank.acc.fasta.new.xz
 mv cncb.nonGenBank.acc.fasta.new.xz cncb.nonGenBank.acc.fasta.xz
 
 xzcat cncb.nonGenBank.acc.fasta.xz \
 | faSomeRecords stdin <(cut -f 1 accToNameBarAcc.tsv) stdout \
 | faRenameRecords stdin accToNameBarAcc.tsv cncb.nonGenBank.fasta
 
 # Run nextclade
 cp ../cncb.latest/nextclade.full.tsv.gz .
 cp ../cncb.latest/nextclade.tsv .
 if [ -s new.accs.fa ]; then
     nDataDir=~angie/github/nextclade/data/sars-cov-2
     time nextclade run -j 20 new.accs.fa \
         --input-dataset $nDataDir \
-        --output-fasta nextalign.fa.xz \
+        --output-fasta nextalign.new.fa.xz \
         --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