265430be8faea69b3c41caa789e9a58a0ac4ebb8
angie
  Fri Dec 20 15:25:04 2024 -0800
Suppress progressbar when downloading, clean up when done.

diff --git src/hg/utils/otto/dengue/getNcbiDengue.sh src/hg/utils/otto/dengue/getNcbiDengue.sh
index f591004..ba7c5c2 100755
--- src/hg/utils/otto/dengue/getNcbiDengue.sh
+++ src/hg/utils/otto/dengue/getNcbiDengue.sh
@@ -38,44 +38,46 @@
         # Double the delay to give NCBI progressively more time
         retryDelay=$(($retryDelay * 2))
     fi
 done
 if [[ ! -f metadata.tsv ]]; then
     echo "datasets command failed $maxAttempts times; quitting."
     exit 1
 fi
 wc -l metadata.tsv
 
 attempt=0
 maxAttempts=5
 retryDelay=300
 while [[ $((++attempt)) -le $maxAttempts ]]; do
     echo "fasta attempt $attempt"
-    if datasets download virus genome taxon $taxId --include genome,biosample; then
+    if datasets download virus --no-progressbar genome taxon $taxId --include genome,biosample; then
         break;
     else
         echo "FAILED fasta; will try again after $retryDelay seconds"
         rm -f ncbi_dataset.zip
         sleep $retryDelay
         # Double the delay to give NCBI progressively more time
         retryDelay=$(($retryDelay * 2))
     fi
 done
 if [[ ! -s ncbi_dataset.zip ]]; then
     echo "fasta query failed $maxAttempts times; quitting."
     exit 1
 fi
 unzip ncbi_dataset.zip
 faFilter -minSize=$minSize ncbi_dataset/data/genomic.fna stdout \
 | xz -T 20 > genbank.fa.xz
 faSize <(xzcat genbank.fa.xz)
 
 # Make sure the download wasn't truncated without reporting an error:
 count=$(wc -l < metadata.tsv)
 minSamples=12000
 if (( $count < $minSamples )); then
     echo "*** Too few samples ($count)!  Expected at least $minSamples.  Halting. ***"
     exit 1
 fi
 
+rm -rf ncbi_dataset ncbi_dataset.zip
+
 rm -f $dengueDir/ncbi/ncbi.latest
 ln -s ncbi.$today $dengueDir/ncbi/ncbi.latest