diff --git a/java/common/pom.xml b/java/common/pom.xml
index 915ec3a..75f191a 100644
--- a/java/common/pom.xml
+++ b/java/common/pom.xml
@@ -6,7 +6,7 @@
 
     <groupId>com.debricked</groupId>
     <artifactId>SootWrapper</artifactId>
-    <version>5.0</version>
+    <version>5.1</version>
 
     <properties>
         <maven.compiler.source>11</maven.compiler.source>
@@ -23,7 +23,7 @@
         <dependency>
             <groupId>org.soot-oss</groupId>
             <artifactId>soot</artifactId>
-            <version>4.2.1</version>
+            <version>4.4.1</version>
         </dependency>
         <dependency>
             <groupId>info.picocli</groupId>
diff --git a/java/common/src/main/java/SootWrapper/Cli.java b/java/common/src/main/java/SootWrapper/Cli.java
index d7804f1..253c373 100644
--- a/java/common/src/main/java/SootWrapper/Cli.java
+++ b/java/common/src/main/java/SootWrapper/Cli.java
@@ -34,8 +34,8 @@ public static void main(String[] args) {
 
     @Override
     public Integer call() throws Exception {
-        checkExistsAndIsDir(userCodePaths);
-        checkExistsAndIsDir(libraryCodePaths);
+        checkExistsAndIsDir(userCodePaths, true);
+        checkExistsAndIsDir(libraryCodePaths, false);
         BufferedWriter writer;
         if (outputFile != null) {
             if (outputFile.isDirectory()) {
@@ -85,13 +85,25 @@ public Integer call() throws Exception {
         return exitCode;
     }
 
-    private static void checkExistsAndIsDir(Iterable<? extends Path> paths) throws FileNotFoundException {
+    private static void checkExistsAndIsDir(Iterable<? extends Path> paths, boolean checkJar) throws FileNotFoundException {
         for (Path p : paths) {
             File f = p.toFile();
             if (!f.exists()) {
                 throw new FileNotFoundException(String.format("Error: %s can't be found", p));
             }
             if (!f.isDirectory()) {
+                // Check for .jar file
+                if (checkJar) {
+                    String fileName = f.getName();
+                    int index = fileName.lastIndexOf('.');
+                    if (index > 0) {
+                        String extension = fileName.substring(index+1);
+                        if (extension.equals("jar")) {
+                            return;
+                        }
+                    }
+                }
+
                 throw new IllegalArgumentException(String.format("Error: %s is not a directory", p));
             }
         }
diff --git a/java/common/src/test/java/SootWrapper/SootWrapperTest.java b/java/common/src/test/java/SootWrapper/SootWrapperTest.java
index ed5bbb3..5d65d3e 100644
--- a/java/common/src/test/java/SootWrapper/SootWrapperTest.java
+++ b/java/common/src/test/java/SootWrapper/SootWrapperTest.java
@@ -256,7 +256,7 @@ public void testGetCallGraphSelf() {
                     "SootWrapper.Cli.main(String[])"
             });
             assertMethodIsCalledByMethods(calls, "java.io.File.exists()", new String[]{
-                    "SootWrapper.Cli.checkExistsAndIsDir(Iterable)"
+                    "SootWrapper.Cli.checkExistsAndIsDir(Iterable, boolean)"
             });
             assertMethodIsCalledByMethods(calls, "soot.G.reset()", new String[]{
                     "SootWrapper.SootWrapper.writeAnalysis(JSONWriter, Iterable, Iterable)"