diff --git a/cmd/gosec/main.go b/cmd/gosec/main.go
index d740aa0..83e7692 100644
--- a/cmd/gosec/main.go
+++ b/cmd/gosec/main.go
@@ -318,7 +318,11 @@ func main() {
 		os.Exit(0)
 	}
 
-	rootPath := packages[0]
+	rootPath, err := gosec.RootPath(flag.Args()[0])
+	if err != nil {
+		logger.Fatalf("Failed to get the root path of the project: %s", err)
+	}
+
 	// Create output report
 	if err := saveOutput(*flagOutput, *flagFormat, rootPath, issues, metrics, errors); err != nil {
 		logger.Fatal(err)
diff --git a/helpers.go b/helpers.go
index b2e5176..3fddae3 100644
--- a/helpers.go
+++ b/helpers.go
@@ -387,3 +387,11 @@ func PackagePaths(root string, exclude *regexp.Regexp) ([]string, error) {
 	}
 	return result, nil
 }
+
+// RootPath returns the absolute root path of a scan
+func RootPath(root string) (string, error) {
+	if strings.HasSuffix(root, "...") {
+		root = root[0 : len(root)-3]
+	}
+	return filepath.Abs(root)
+}
diff --git a/helpers_test.go b/helpers_test.go
index 636ef6d..f797203 100644
--- a/helpers_test.go
+++ b/helpers_test.go
@@ -3,6 +3,7 @@ package gosec_test
 import (
 	"io/ioutil"
 	"os"
+	"path/filepath"
 	"regexp"
 
 	. "github.com/onsi/ginkgo"
@@ -53,4 +54,23 @@ var _ = Describe("Helpers", func() {
 			Expect(paths).Should(BeEmpty())
 		})
 	})
+
+	Context("when getting the root path", func() {
+		It("should return the absolute path from relative path", func() {
+			base := "test"
+			cwd, err := os.Getwd()
+			Expect(err).ShouldNot(HaveOccurred())
+			root, err := gosec.RootPath(base)
+			Expect(err).ShouldNot(HaveOccurred())
+			Expect(root).Should(Equal(filepath.Join(cwd, base)))
+		})
+		It("should retrun the absolute path from ellipsis path", func() {
+			base := "test"
+			cwd, err := os.Getwd()
+			Expect(err).ShouldNot(HaveOccurred())
+			root, err := gosec.RootPath(filepath.Join(base, "..."))
+			Expect(err).ShouldNot(HaveOccurred())
+			Expect(root).Should(Equal(filepath.Join(cwd, base)))
+		})
+	})
 })
diff --git a/output/formatter.go b/output/formatter.go
index e29664c..a63b51f 100644
--- a/output/formatter.go
+++ b/output/formatter.go
@@ -105,19 +105,32 @@ func CreateReport(w io.Writer, format, rootPath string, issues []*gosec.Issue, m
 }
 
 func reportSonarqube(rootPath string, w io.Writer, data *reportInfo) error {
+	si, err := convertToSonarIssues(rootPath, data)
+	if err != nil {
+		return err
+	}
+	raw, err := json.MarshalIndent(si, "", "\t")
+	if err != nil {
+		return err
+	}
+	_, err = w.Write(raw)
+	return err
+}
+
+func convertToSonarIssues(rootPath string, data *reportInfo) (sonarIssues, error) {
 	var si sonarIssues
 	for _, issue := range data.Issues {
 		lines := strings.Split(issue.Line, "-")
 
 		startLine, err := strconv.Atoi(lines[0])
 		if err != nil {
-			return err
+			return si, err
 		}
 		endLine := startLine
 		if len(lines) > 1 {
 			endLine, err = strconv.Atoi(lines[1])
 			if err != nil {
-				return err
+				return si, err
 			}
 		}
 		s := sonarIssue{
@@ -134,12 +147,7 @@ func reportSonarqube(rootPath string, w io.Writer, data *reportInfo) error {
 		}
 		si.SonarIssues = append(si.SonarIssues, s)
 	}
-	raw, err := json.MarshalIndent(si, "", "\t")
-	if err != nil {
-		return err
-	}
-	_, err = w.Write(raw)
-	return err
+	return si, nil
 }
 
 func reportJSON(w io.Writer, data *reportInfo) error {
diff --git a/output/formatter_suite_test.go b/output/formatter_suite_test.go
new file mode 100644
index 0000000..62b1404
--- /dev/null
+++ b/output/formatter_suite_test.go
@@ -0,0 +1,13 @@
+package output
+
+import (
+	. "github.com/onsi/ginkgo"
+	. "github.com/onsi/gomega"
+
+	"testing"
+)
+
+func TestRules(t *testing.T) {
+	RegisterFailHandler(Fail)
+	RunSpecs(t, "Formatters Suite")
+}
diff --git a/output/formatter_test.go b/output/formatter_test.go
new file mode 100644
index 0000000..1d016f6
--- /dev/null
+++ b/output/formatter_test.go
@@ -0,0 +1,110 @@
+package output
+
+import (
+	. "github.com/onsi/ginkgo"
+	. "github.com/onsi/gomega"
+
+	"github.com/securego/gosec"
+)
+
+var _ = Describe("Formatter", func() {
+	BeforeEach(func() {
+	})
+	Context("when converting to Sonarqube issues", func() {
+		It("it should parse the report info", func() {
+			data := &reportInfo{
+				Errors: map[string][]gosec.Error{},
+				Issues: []*gosec.Issue{
+					&gosec.Issue{
+						Severity:   2,
+						Confidence: 0,
+						RuleID:     "test",
+						What:       "test",
+						File:       "/home/src/project/test.go",
+						Code:       "",
+						Line:       "1-2",
+					},
+				},
+				Stats: &gosec.Metrics{
+					NumFiles: 0,
+					NumLines: 0,
+					NumNosec: 0,
+					NumFound: 0,
+				},
+			}
+			want := sonarIssues{
+				SonarIssues: []sonarIssue{
+					{
+						EngineID: "gosec",
+						RuleID:   "test",
+						PrimaryLocation: location{
+							Message:  "test",
+							FilePath: "test.go",
+							TextRange: textRange{
+								StartLine: 1,
+								EndLine:   2,
+							},
+						},
+						Type:          "VULNERABILITY",
+						Severity:      "BLOCKER",
+						EffortMinutes: SonarqubeEffortMinutes,
+					},
+				},
+			}
+
+			rootPath := "/home/src/project"
+
+			issues, err := convertToSonarIssues(rootPath, data)
+			Expect(err).ShouldNot(HaveOccurred())
+			Expect(issues).To(Equal(want))
+		})
+
+		It("it should parse the report info with files in subfolders", func() {
+			data := &reportInfo{
+				Errors: map[string][]gosec.Error{},
+				Issues: []*gosec.Issue{
+					&gosec.Issue{
+						Severity:   2,
+						Confidence: 0,
+						RuleID:     "test",
+						What:       "test",
+						File:       "/home/src/project/subfolder/test.go",
+						Code:       "",
+						Line:       "1-2",
+					},
+				},
+				Stats: &gosec.Metrics{
+					NumFiles: 0,
+					NumLines: 0,
+					NumNosec: 0,
+					NumFound: 0,
+				},
+			}
+			want := sonarIssues{
+				SonarIssues: []sonarIssue{
+					{
+						EngineID: "gosec",
+						RuleID:   "test",
+						PrimaryLocation: location{
+							Message:  "test",
+							FilePath: "subfolder/test.go",
+							TextRange: textRange{
+								StartLine: 1,
+								EndLine:   2,
+							},
+						},
+						Type:          "VULNERABILITY",
+						Severity:      "BLOCKER",
+						EffortMinutes: SonarqubeEffortMinutes,
+					},
+				},
+			}
+
+			rootPath := "/home/src/project"
+
+			issues, err := convertToSonarIssues(rootPath, data)
+			Expect(err).ShouldNot(HaveOccurred())
+			Expect(issues).To(Equal(want))
+		})
+	})
+})