diff --git a/piranha/input_parsing/initialising.py b/piranha/input_parsing/initialising.py
index 1e9e689..e4bb13b 100644
--- a/piranha/input_parsing/initialising.py
+++ b/piranha/input_parsing/initialising.py
@@ -30,6 +30,7 @@ def get_defaults():
                     KEY_OVERWRITE:False,
                     KEY_REFERENCES_FOR_CNS:VALUE_REFERENCES_FOR_CNS,
                     KEY_SUMMARY_HEADERS: VALUE_SUMMARY_HEADERS,
+                    KEY_ARCHIVE_FASTQ:False,
 
                     # input seq options
                     KEY_SAMPLE_TYPE:VALUE_SAMPLE_TYPE,  #options are stool or environmental