diff --git a/src/nf_modules/gffread/main.nf b/src/nf_modules/gffread/main.nf
index 07e010e71329313b45b73cc8f827368c9dba2cc5..3f7a4db4bf7118b61b90c6d23bcf147c62436a99 100644
--- a/src/nf_modules/gffread/main.nf
+++ b/src/nf_modules/gffread/main.nf
@@ -26,6 +26,6 @@ process gffread {
   }
   """
   gffread ${gtf} -g ${fasta} -M -x dup_${file_prefix}.fasta
-  awk 'BEGIN {i = 1;} { if (\$1 ~ /^>/) { tmp = h[i]; h[i] = \$1; } else if (!a[\$1]) { s[i] = \$1; a[\$1] = "1"; i++; } else { h[i] = tmp; } } END { for (j = 1; j < i; j++) { print h[j]; print s[j]; } }' < dup_${file_prefix}.fasta > ${file_prefix}.fasta
+  awk 'BEGIN {i = 1;} { if (\$1 ~ /^>/) { tmp = h[i]; h[i] = \$1; } else if (!a[\$1]) { s[i] = \$1; a[\$1] = "1"; i++; } else { h[i] = tmp; } } END { for (j = 1; j < i; j++) { print h[j]; print s[j]; } }' < dup_${file_prefix}.fasta | grep -v -e "^\$" > ${file_prefix}.fasta
   """
 }