diff --git a/Pipfile b/Pipfile
index a9d403d..80785b2 100644
--- a/Pipfile
+++ b/Pipfile
@@ -10,7 +10,7 @@ python-levenshtein = "==0.12.0"
 pandas = "==2.0.2"
 requests = "==2.31.0"
 pyyaml = "*"
-intactness-pipeline = {ref = "cfe-1.2", git = "https://github.com/cfe-lab/HIVIntact"}
+intactness-pipeline = {ref = "cfe-1.3", git = "https://github.com/cfe-lab/HIVIntact"}
 
 [dev-packages]
 pytest = "*"
diff --git a/Pipfile.lock b/Pipfile.lock
index aed6c1c..840919c 100644
--- a/Pipfile.lock
+++ b/Pipfile.lock
@@ -1,7 +1,7 @@
 {
     "_meta": {
         "hash": {
-            "sha256": "100f2cea5bdbda87105a66b042daed34e24cc3e092e8382794b6f03c5553b02d"
+            "sha256": "c5e8c3f18599c2490183a8f39736737ebf0b47821cc0908a613f2e95e8ee8684"
         },
         "pipfile-spec": 6,
         "requires": {
@@ -165,7 +165,7 @@
         },
         "intactness-pipeline": {
             "git": "https://github.com/cfe-lab/HIVIntact",
-            "ref": "14f571d873131d2521a6bddcefbf795914ac78c7"
+            "ref": "2bb83a07b42e78a08c0f40a971d06f9393795717"
         },
         "jarowinkler": {
             "hashes": [
@@ -342,7 +342,7 @@
                 "sha256:0123cacc1627ae19ddf3c27a5de5bd67ee4586fbdd6440d9748f8abb483d3e86",
                 "sha256:961d03dc3453ebbc59dbdea9e4e11c5651520a876d0f4db161e8674aae935da9"
             ],
-            "markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'",
+            "markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2'",
             "version": "==2.8.2"
         },
         "python-levenshtein": {
@@ -451,7 +451,7 @@
                 "sha256:1e61c37477a1626458e36f7b1d82aa5c9b094fa4802892072e49de9c60c4c926",
                 "sha256:8abb2f1d86890a2dfb989f9a77cfcfd3e47c2a354b01111771326f8aa26e0254"
             ],
-            "markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'",
+            "markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2'",
             "version": "==1.16.0"
         },
         "tzdata": {
diff --git a/Singularity b/Singularity
index 5f18945..83379d4 100644
--- a/Singularity
+++ b/Singularity
@@ -38,7 +38,7 @@ From: ubuntu:22.04
     apt-get install -y ncbi-blast+
 
     echo ===== Installing Python packages ===== >/dev/null
-    pip3 install git+https://github.com/cfe-lab/HIVIntact@cfe-1.2
+    pip3 install git+https://github.com/cfe-lab/HIVIntact@cfe-1.3
 
     cd /opt/primer_finder
     pip3 install .
diff --git a/setup.py b/setup.py
index 8fc0cd8..42a0f7d 100644
--- a/setup.py
+++ b/setup.py
@@ -10,7 +10,7 @@
         'python-Levenshtein==0.12.0',
         'pandas==2.0.2',
         'requests==2.31.0',
-        'intactness-pipeline @ git+https://github.com/cfe-lab/HIVIntact.git@cfe-1.2',
+        'intactness-pipeline @ git+https://github.com/cfe-lab/HIVIntact.git@cfe-1.3',
         'pyyaml'
     ],
     package_data={