diff --git a/tasks/basecalling/task_dorado_demux.wdl b/tasks/basecalling/task_dorado_demux.wdl
index b926aeed1..50ee4deee 100644
--- a/tasks/basecalling/task_dorado_demux.wdl
+++ b/tasks/basecalling/task_dorado_demux.wdl
@@ -16,7 +16,7 @@ task dorado_demux {
     set -euo pipefail
 
     # Capture Dorado version
-    dorado --version | tee DORADO_VERSION
+    dorado --version 2>&1 | tee DORADO_VERSION
     echo "Dorado version:" $(cat DORADO_VERSION)
 
     # Output the Dorado model used
diff --git a/tasks/basecalling/task_samtools_convert.wdl b/tasks/basecalling/task_samtools_convert.wdl
index c164d7982..a25f826e1 100644
--- a/tasks/basecalling/task_samtools_convert.wdl
+++ b/tasks/basecalling/task_samtools_convert.wdl
@@ -13,7 +13,7 @@ task samtools_convert {
     set -euo pipefail
 
     # samtools version
-    samtools --version | tee SAMTOOLS_VERSION
+    samtools --version | head -n1 | tee VERSION
 
     bam_output="output/bam/"
     mkdir -p "$bam_output"