diff --git a/README.md b/README.md
index 4ca7db3ca2716d903e92ac77291a8f2c670c6ac8..d39bab117a9c77c388f944a5ef5fc99e74e1e975 100644
--- a/README.md
+++ b/README.md
@@ -122,6 +122,8 @@ This pipeline is also capable of being run on AWS and DNAnexus. To do so:
     --instance-type mem1_ssd1_v2_x16 \
     --input-json "$(envsubst < ./docs/nxf_dnanexus-ci-test.json)"
   ```
+### NOTE:
+* File locations used in cloud deployments (auth files and output folder) need to be accessible in that environment (eg s3 location, or DNAnexus location). Local paths cannot be read local locations.
 <hr>
 To generate you own references or new references:
 ------------------------------------------