From 7db4a760766b240406b124ed141e8c069c297396 Mon Sep 17 00:00:00 2001
From: Lee Katz <gzu2@cdc.gov>
Date: Wed, 10 Apr 2024 15:49:54 -0400
Subject: [PATCH] downloadKalamari.pl: add in retmax 1

---
 bin/downloadKalamari.pl | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/bin/downloadKalamari.pl b/bin/downloadKalamari.pl
index 040467b..5b30463 100644
--- a/bin/downloadKalamari.pl
+++ b/bin/downloadKalamari.pl
@@ -79,7 +79,8 @@ sub downloadEntry{
   # Get the esearch xml in place for at least one downstream query
   my $esearchXml = "$dir/$acc.esearch.xml";
   if(! -e $esearchXml){
-    system("esearch -db nuccore -query '$acc' > $esearchXml.tmp");
+    # -retmax 1 to help avoid refseq/INSDC conflation
+    system("esearch -db nuccore -query '$acc' -retmax 1 > $esearchXml.tmp");
     if($?){
       die "ERROR running esearch: $!";
     }