diff --git a/etc/run_blastn.sanger b/etc/run_blastn.sanger
index 0a10e01ad9c7cd2b2510ec8fb47c9654c36f1862..4ecc72845825a6e1c314a6bf2361599259b955ba 100755
--- a/etc/run_blastn.sanger
+++ b/etc/run_blastn.sanger
@@ -86,7 +86,7 @@ run_one_prog () {
     fi
 
     #### end of changes
-    while [ ! -f $OUTPUT_FILE ]; do sleep 2; done
+    count=0; while  (test ! -f $OUTPUT_FILE)  && (test $count -lt 1000) ; do sleep 2; count+=1; done
 
     if [ -s ${PROG}_errors.new ]
     then