From fb3ce4695c888d87d60c7b6aba3df6c2ace1dea2 Mon Sep 17 00:00:00 2001
From: Yossi Farjoun <yossi@fulcrumgenomics.com>
Date: Fri, 28 Jun 2024 12:09:27 -0400
Subject: [PATCH] Update Bams.scala

---
 src/main/scala/com/fulcrumgenomics/bam/Bams.scala | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/main/scala/com/fulcrumgenomics/bam/Bams.scala b/src/main/scala/com/fulcrumgenomics/bam/Bams.scala
index 623b97d76..54353f17d 100644
--- a/src/main/scala/com/fulcrumgenomics/bam/Bams.scala
+++ b/src/main/scala/com/fulcrumgenomics/bam/Bams.scala
@@ -542,7 +542,7 @@ object Bams extends LazyLogging {
       "Input was not queryname sorted or query grouped, found: " +
         s"SO:${header.getSortOrder} GO:${header.getGroupOrder}" +
         Option(header.getAttribute("SS")).map(ss => f" SS:$ss").getOrElse("") +
-        f". Use `samtools sort -n -u in.bam | fgbio $toolName -i /dev/stdin`" +
+        f". Use `samtools sort -n in.bam | fgbio $toolName -i /dev/stdin`" +
         path.map(p => f"\nPath: $p").getOrElse("")
     )
   }