abdea7a81b3d511adaee6300277721a804f5581f
angie
  Tue Mar 30 11:57:47 2021 -0700
Ongoing fixes for odd characters in sequence names and other pipeline tweaks.

diff --git src/hg/utils/otto/sarscov2phylo/getNcbi.sh src/hg/utils/otto/sarscov2phylo/getNcbi.sh
index 96e63f0..b7186aa 100755
--- src/hg/utils/otto/sarscov2phylo/getNcbi.sh
+++ src/hg/utils/otto/sarscov2phylo/getNcbi.sh
@@ -8,31 +8,31 @@
 # Use enhanced metadata to rewrite FASTA headers for matching up with sequences in other databases.
 
 scriptDir=$(dirname "${BASH_SOURCE[0]}")
 source $scriptDir/util.sh
 
 today=$(date +%F)
 prevDate=$(date -d yesterday +%F)
 
 ottoDir=/hive/data/outside/otto/sarscov2phylo
 
 mkdir -p $ottoDir/ncbi.$today
 cd $ottoDir/ncbi.$today
 
 # This query gives a large zip file that includes extra stuff, and the download really slows
 # down after a point, but it does provide a consistent set of FASTA and metadata:
-time curl -s -X GET \
+time curl -sS -X GET \
     "https://api.ncbi.nlm.nih.gov/datasets/v1alpha/virus/taxon/2697049/genome/download?refseq_only=false&annotated_only=false&released_since=2020-01-01&complete_only=false&include_annotation_type=DEFAULT&filename=ncbi_dataset.$today.zip" \
     -H "Accept: application/zip" \
     > ncbi_dataset.zip
 
 rm -rf ncbi_dataset
 unzip ncbi_dataset.zip
 # Creates ./ncbi_dataset/
 
 # This makes something just like ncbi.datasets.tsv from the /table/ API query:
 jq -c -r '[.accession, .biosample, .isolate.collectionDate, .location.geographicLocation, .host.sciName, .isolate.name, .completeness, (.length|tostring)] | join("\t")' \
     ncbi_dataset/data/data_report.jsonl \
 | sed -e 's/COMPLETE/complete/; s/PARTIAL/partial/;' \
 | sort \
     > ncbi_dataset.tsv