diff --git a/cmd/compile_test.go b/cmd/compile_test.go
index 42c8a93..9ce15d5 100644
--- a/cmd/compile_test.go
+++ b/cmd/compile_test.go
@@ -75,3 +75,45 @@ func TestCompileCmd_Good(t *testing.T) {
 		t.Error("rootfs/test.txt not found in matrix")
 	}
 }
+
+func TestCompileCmd_Bad_InvalidBorgfile(t *testing.T) {
+	tempDir := t.TempDir()
+	borgfilePath := filepath.Join(tempDir, "Borgfile")
+	outputMatrixPath := filepath.Join(tempDir, "test.matrix")
+
+	// Create a dummy Borgfile with an invalid instruction.
+	borgfileContent := "INVALID_INSTRUCTION"
+	err := os.WriteFile(borgfilePath, []byte(borgfileContent), 0644)
+	if err != nil {
+		t.Fatalf("failed to create Borgfile: %v", err)
+	}
+
+	// Run the compile command.
+	rootCmd := NewRootCmd()
+	rootCmd.AddCommand(compileCmd)
+	_, err = executeCommand(rootCmd, "compile", "-f", borgfilePath, "-o", outputMatrixPath)
+	if err == nil {
+		t.Fatal("compile command should have failed but did not")
+	}
+}
+
+func TestCompileCmd_Bad_MissingInputFile(t *testing.T) {
+	tempDir := t.TempDir()
+	borgfilePath := filepath.Join(tempDir, "Borgfile")
+	outputMatrixPath := filepath.Join(tempDir, "test.matrix")
+
+	// Create a dummy Borgfile that references a non-existent file.
+	borgfileContent := "ADD /non/existent/file /test.txt"
+	err := os.WriteFile(borgfilePath, []byte(borgfileContent), 0644)
+	if err != nil {
+		t.Fatalf("failed to create Borgfile: %v", err)
+	}
+
+	// Run the compile command.
+	rootCmd := NewRootCmd()
+	rootCmd.AddCommand(compileCmd)
+	_, err = executeCommand(rootCmd, "compile", "-f", borgfilePath, "-o", outputMatrixPath)
+	if err == nil {
+		t.Fatal("compile command should have failed but did not")
+	}
+}
diff --git a/cmd/run_test.go b/cmd/run_test.go
index bec33fc..4b93c09 100644
--- a/cmd/run_test.go
+++ b/cmd/run_test.go
@@ -75,3 +75,13 @@ func TestRunCmd_Good(t *testing.T) {
 		t.Fatalf("run command failed: %v", err)
 	}
 }
+
+func TestRunCmd_Bad_MissingInputFile(t *testing.T) {
+	// Run the run command with a non-existent file.
+	rootCmd := NewRootCmd()
+	rootCmd.AddCommand(runCmd)
+	_, err := executeCommand(rootCmd, "run", "/non/existent/file.matrix")
+	if err == nil {
+		t.Fatal("run command should have failed but did not")
+	}
+}
diff --git a/pkg/matrix/matrix_test.go b/pkg/matrix/matrix_test.go
new file mode 100644
index 0000000..6c6567c
--- /dev/null
+++ b/pkg/matrix/matrix_test.go
@@ -0,0 +1,88 @@
+package matrix
+
+import (
+	"archive/tar"
+	"bytes"
+	"testing"
+
+	"github.com/Snider/Borg/pkg/datanode"
+)
+
+func TestNew(t *testing.T) {
+	m, err := New()
+	if err != nil {
+		t.Fatalf("New() returned an error: %v", err)
+	}
+	if m == nil {
+		t.Fatal("New() returned a nil matrix")
+	}
+	if m.Config == nil {
+		t.Error("New() returned a matrix with a nil config")
+	}
+	if m.RootFS == nil {
+		t.Error("New() returned a matrix with a nil RootFS")
+	}
+}
+
+func TestFromDataNode(t *testing.T) {
+	dn := datanode.New()
+	dn.AddData("test.txt", []byte("hello world"))
+	m, err := FromDataNode(dn)
+	if err != nil {
+		t.Fatalf("FromDataNode() returned an error: %v", err)
+	}
+	if m == nil {
+		t.Fatal("FromDataNode() returned a nil matrix")
+	}
+	if m.RootFS != dn {
+		t.Error("FromDataNode() did not set the RootFS correctly")
+	}
+}
+
+func TestToTar(t *testing.T) {
+	m, err := New()
+	if err != nil {
+		t.Fatalf("New() returned an error: %v", err)
+	}
+	m.RootFS.AddData("test.txt", []byte("hello world"))
+	tarball, err := m.ToTar()
+	if err != nil {
+		t.Fatalf("ToTar() returned an error: %v", err)
+	}
+	if tarball == nil {
+		t.Fatal("ToTar() returned a nil tarball")
+	}
+
+	tr := tar.NewReader(bytes.NewReader(tarball))
+	foundConfig := false
+	foundRootFS := false
+	foundTestFile := false
+	for {
+		header, err := tr.Next()
+		if err != nil {
+			if err.Error() == "EOF" {
+				break
+			}
+			t.Fatalf("failed to read tar header: %v", err)
+		}
+
+		switch header.Name {
+		case "config.json":
+			foundConfig = true
+		case "rootfs/":
+			foundRootFS = true
+		case "rootfs/test.txt":
+			foundTestFile = true
+		}
+	}
+
+	if !foundConfig {
+		t.Error("config.json not found in matrix")
+	}
+	if !foundRootFS {
+		t.Error("rootfs/ not found in matrix")
+	}
+	if !foundTestFile {
+		t.Error("rootfs/test.txt not found in matrix")
+	}
+}