diff --git a/CHANGELOG.md b/CHANGELOG.md
index 0fa6ea58..f96079c1 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -12,6 +12,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - Fix singularity image pull tag for MAGeCKFlute ([#160](https://github.com/nf-core/crisprseq/pull/160))
 - Skip dolar signs on containerOptions ([#163](https://github.com/nf-core/crisprseq/pull/163))
 - Fix error in R script when adding patterns ([#170](https://github.com/nf-core/crisprseq/pull/170))
+- Skip MAGeCKFlute when the function produces an error within the R package
 
 ### Deprecated
 
diff --git a/templates/template_fluteMLE.R b/templates/template_fluteMLE.R
index 1a9c10fd..015e4457 100644
--- a/templates/template_fluteMLE.R
+++ b/templates/template_fluteMLE.R
@@ -17,14 +17,28 @@
         before_beta <- sub("\\\\.beta.*", "", beta_strings)
         unique_strings <- unique(before_beta)
         for(i in unique_strings) {
-            FluteMLE(mle, treatname= i, proj=i, pathview.top=5)
-            }
+            tryCatch(
+                {
+                    FluteMLE(mle, treatname= i, proj=i, pathview.top=5)
+                },
+            error=function(e) {
+                    print(paste0("Could not run FluteMLE with project ",i))
+                }
+            )
+        }
     } else {
         beta_strings <- grep("\\\\.beta", colnames(mle), value = TRUE)
         before_beta <- sub("\\\\.beta.*", "", beta_strings)
         unique_strings <- unique(before_beta)
         for(i in unique_strings) {
-            FluteMLE(mle, treatname= i, proj=i, ${args}, pathview.top=5)
+            tryCatch(
+                {
+                FluteMLE(mle, treatname= i, proj=i, ${args}, pathview.top=5)
+                },
+            error=function(e) {
+                    print(paste0("Could not run FluteMLE with project ",i))
+                }
+            )
         }
     }