diff --git a/rna-seq.nf b/rna-seq.nf
index e3244cc44f74279f81ce0ad73c470f7e38369520..79a325138a272ffe0866403910c42f88038b949b 100644
--- a/rna-seq.nf
+++ b/rna-seq.nf
@@ -441,6 +441,7 @@ process parseMetadata {
     fi
     if [ "${params.endsForce}" != "" ]
     then
+      fastqCountError=false
       fastqReadError=false
       fastqReadError_details=""
     fi