diff --git a/dev/phpunit/functional/FunctionalTests.php b/dev/phpunit/functional/FunctionalTests.php
index 67a42849..a4ddb7fc 100644
--- a/dev/phpunit/functional/FunctionalTests.php
+++ b/dev/phpunit/functional/FunctionalTests.php
@@ -174,7 +174,7 @@ public function testMagentoTwoFour()
     {
         $this->assertFileExists(BASE_DIR . '/dev/instances/magento24/app/etc/env.php', "Magento 2.4 is not installed");
 
-        exec($this->generateAnalyseCommand('/dev/instances/magento24', '--sort-by-type --vendor-namespaces Ampersand'), $output, $return);
+        exec($this->generateAnalyseCommand('/dev/instances/../instances/magento24', '--sort-by-type --vendor-namespaces Ampersand'), $output, $return);
         $this->assertEquals(0, $return, "The return code of the command was not zero");
 
         $lastLine = array_pop($output);
@@ -204,7 +204,7 @@ public function testMagentoTwoFourNoDb()
         $this->assertFileExists(BASE_DIR . '/dev/instances/magento24nodb/app/etc/di.xml', "Magento 2.4 directory is wrong");
         $this->assertFileNotExists(BASE_DIR . '/dev/instances/magento24nodb/app/etc/env.php', "Magento 2.4 is installed when it shouldnt be");
 
-        exec($this->generateAnalyseCommand('/dev/instances/magento24nodb', '--sort-by-type --vendor-namespaces Ampersand'), $output, $return);
+        exec($this->generateAnalyseCommand('/dev/instances/../instances/magento24nodb', '--sort-by-type --vendor-namespaces Ampersand'), $output, $return);
         $this->assertEquals(0, $return, "The return code of the command was not zero");
 
         $lastLine = array_pop($output);
diff --git a/src/Ampersand/PatchHelper/Command/AnalyseCommand.php b/src/Ampersand/PatchHelper/Command/AnalyseCommand.php
index 49093022..feee8662 100644
--- a/src/Ampersand/PatchHelper/Command/AnalyseCommand.php
+++ b/src/Ampersand/PatchHelper/Command/AnalyseCommand.php
@@ -90,7 +90,7 @@ protected function execute(InputInterface $input, OutputInterface $output)
                         $patchFilesToOutput[$file] = $patchFile;
                     }
                     foreach ($errors as $error) {
-                        $summaryOutputData[] = [$errorType, $file, ltrim(str_replace($projectDir, '', $error), '/')];
+                        $summaryOutputData[] = [$errorType, $file, ltrim(str_replace(realpath($projectDir), '', $error), '/')];
                         if ($errorType === Helper\PatchOverrideValidator::TYPE_FILE_OVERRIDE
                             && $input->getOption('auto-theme-update') && is_numeric($input->getOption('auto-theme-update'))) {
                             $patchFile->applyToTheme($projectDir, $error, $input->getOption('auto-theme-update'));