diff --git a/preprocessor/cactus_sanitizeFastaHeaders.c b/preprocessor/cactus_sanitizeFastaHeaders.c
index c73294117..8f69a2119 100644
--- a/preprocessor/cactus_sanitizeFastaHeaders.c
+++ b/preprocessor/cactus_sanitizeFastaHeaders.c
@@ -128,6 +128,17 @@ void addUniqueFastaPrefix(void* destination, const char *fastaHeader, const char
         clipped_header = prefixed_header;
     }
     
+    // sanity check
+    int64_t n = strlen(string);
+    for (int64_t i = 0; i < n; ++i) {
+        char c = tolower(string[i]);
+        if (c != 'a' && c != 'c' && c != 'g' && c != 't' && c != 'n') {
+            fprintf(stderr, "Error: Non-ACGTN character '%c' found at position %" PRIi64 " of FASTA sequence %s in event %s\n",
+                    c, i, fastaHeader, eventName);
+            exit(1);
+        }
+    }
+    
     fastaWrite((char*)string, clipped_header, stdout);
     free(clipped_header);
 }
diff --git a/submodules/paffy b/submodules/paffy
index 5a71703d2..115c01abc 160000
--- a/submodules/paffy
+++ b/submodules/paffy
@@ -1 +1 @@
-Subproject commit 5a71703d2f0ee0f592e6c2bbf40a00ec6c9ee5ef
+Subproject commit 115c01abcfe01bfb7a7a03317b32ca6d88d84e69