diff --git a/go/extractor/extractor.go b/go/extractor/extractor.go
index fa3f6b7c00d..b4d4815f15c 100644
--- a/go/extractor/extractor.go
+++ b/go/extractor/extractor.go
@@ -814,12 +814,12 @@ func (extraction *Extraction) extractFileInfo(tw *trap.Writer, file string, isDu
 			displayPath = rawPath
 		}
 		if i == len(components)-1 {
-			lbl := tw.Labeler.FileLabelFor(file)
+			lbl := tw.Labeler.FileLabelFor(path)
 			dbscheme.FilesTable.Emit(tw, lbl, displayPath)
 			dbscheme.ContainerParentTable.Emit(tw, parentLbl, lbl)
 			dbscheme.HasLocationTable.Emit(tw, lbl, emitLocation(tw, lbl, 0, 0, 0, 0))
 			extraction.Lock.Lock()
-			slbl := extraction.StatWriter.Labeler.FileLabelFor(file)
+			slbl := extraction.StatWriter.Labeler.FileLabelFor(path)
 			if !isDummy {
 				dbscheme.CompilationCompilingFilesTable.Emit(extraction.StatWriter, extraction.Label, extraction.GetFileIdx(file), slbl)
 			}
diff --git a/go/extractor/trap/labels.go b/go/extractor/trap/labels.go
index 2822da61ff1..9a03bfe9a57 100644
--- a/go/extractor/trap/labels.go
+++ b/go/extractor/trap/labels.go
@@ -4,6 +4,7 @@ import (
 	"fmt"
 	"go/types"
 
+	"github.com/github/codeql-go/extractor/srcarchive"
 	"github.com/github/codeql-go/extractor/util"
 )
 
@@ -67,7 +68,7 @@ func (l *Labeler) GlobalID(key string) Label {
 // FileLabel returns the label for a file with path `path`.
 func (l *Labeler) FileLabel() Label {
 	if l.fileLabel == InvalidLabel {
-		l.fileLabel = l.FileLabelFor(l.tw.path)
+		l.fileLabel = l.FileLabelFor(srcarchive.TransformPath(l.tw.path))
 	}
 	return l.fileLabel
 }