Encountered a fatal error while running "/opt/hostedtoolcache/CodeQL/2.22.1/x64/codeql/codeql database finalize

[Th3S4mur41]

CodeQL with default configuration is failing with the following error

Analyze (javascript-typescript)

Encountered a fatal error while running "/opt/hostedtoolcache/CodeQL/2.22.1/x64/codeql/codeql database finalize --finalize-dataset --threads=2 --ram=6920 --verbosity=progress++ /home/runner/work/_temp/codeql_databases/javascript". 
Exit code was 32 and last log line was: CodeQL detected code written in JavaScript/TypeScript but could not process any of it. 
Check the workflow run logs (see https://docs.github.com/en/actions/monitoring-and-troubleshooting-workflows/using-workflow-run-logs). 

For more information, review our troubleshooting guide at https://gh.io/troubleshooting-code-scanning/no-source-code-seen-during-build . See the logs for more details.

Previous runs on the exact same code with version 2.22.0 didn't face the issue...

Multiple rerun didn't solve the issue either

[mbg]

Hi @Th3S4mur41 👋🏻

Thanks for opening this issue! We will need a bit more information to troubleshoot this. The error you posted is a fairly general error indicating that CodeQL wasn't able to extract any code, but the actual cause for that would likely be further up in the log.

If this is in a public repo, would you be able to link to the workflow run so that I can take a look?

[Th3S4mur41]

Hi @mbg

Unfortunately, not a public repo.

I'd be happy to share more logs with you since the problem is currently reproducible with every run on the branch in question.
If that is not sufficient, I can also raise the ticket internally to have our GitHub contact with access look into it

Here is the full CodeQL Analysis:

Run github/codeql-action/analyze@v3
  with:
    category: /language:javascript-typescript
    output: ../results
    upload: always
    cleanup-level: brutal
    add-snippets: false
    skip-queries: false
    checkout_path: /home/runner/work/components/components
    upload-database: true
    wait-for-processing: true
    token: ***
    matrix: {
    "language": "javascript-typescript",
    "category": "/language:javascript-typescript",
    "build-mode": "none",
    "runner": "[\"ubuntu-latest\"]"
  }
    expect-error: false
  env:
    CODE_SCANNING_REF: refs/pull/937/head
    CODE_SCANNING_BASE_BRANCH: main
    CODE_SCANNING_IS_ANALYZING_DEFAULT_BRANCH: false
    CODE_SCANNING_IS_STEADY_STATE_DEFAULT_SETUP: true
    CODE_SCANNING_WORKFLOW_FILE: 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
    CODEQL_ACTION_FEATURE_MULTI_LANGUAGE: false
    CODEQL_ACTION_FEATURE_SANDWICH: false
    CODEQL_ACTION_FEATURE_SARIF_COMBINE: true
    CODEQL_ACTION_FEATURE_WILL_UPLOAD: true
    CODEQL_ACTION_VERSION: 3.29.1
    JOB_RUN_UUID: 6a972970-97e8-403e-8c9a-f793d3f1296c
    CODEQL_ACTION_INIT_HAS_RUN: true
    CODEQL_ACTION_ANALYSIS_KEY: dynamic/github-code-scanning/codeql:analyze
    CODEQL_WORKFLOW_STARTED_AT: 2025-06-30T07:26:27.211Z
    CODEQL_RAM: 6920
    CODEQL_THREADS: 2
    CODEQL_PROXY_HOST: 
    CODEQL_PROXY_PORT: 
    CODEQL_PROXY_CA_CERTIFICATE: 
    CODEQL_PROXY_URLS: 
While resolving threads, found a cgroup CPUs file with 2 CPUs in /sys/fs/cgroup/cpuset.cpus.effective.
Generating diff range extension pack
  Calculating diff ranges for main...refs/pull/937/head
  Successfully created diff range extension pack at /home/runner/work/_temp/pr-diff-range.
Extracting javascript
  /opt/hostedtoolcache/CodeQL/2.22.1/x64/codeql/codeql database trace-command --use-build-mode --working-dir /home/runner/work/components/components /home/runner/work/_temp/codeql_databases/javascript
  Running command in /home/runner/work/components/components: [/opt/hostedtoolcache/CodeQL/2.22.1/x64/codeql/javascript/tools/autobuild.sh]
  [2025-06-30 07:26:49] [build-stdout] Parallel extraction with 2 threads.
  [2025-06-30 07:26:50] [build-stdout] Found Node.js at: node
  [2025-06-30 07:26:50] [build-stdout] Found Node.js version: v20.19.2
  [2025-06-30 07:26:50] [build-stdout] Opening project /home/runner/work/components/components/tsconfig.json
  [2025-06-30 07:26:50] [build-stdout] Memory for TypeScript process: 3460 MB, and 400 MB reserve
  [2025-06-30 07:26:51] [build-stdout] Done opening project /home/runner/work/components/components/tsconfig.json (1239 ms)
  [2025-06-30 07:26:51] [build-stderr] No JavaScript or TypeScript code found.
Finalizing javascript
  /opt/hostedtoolcache/CodeQL/2.22.1/x64/codeql/codeql database finalize --finalize-dataset --threads=2 --ram=6920 /home/runner/work/_temp/codeql_databases/javascript
  CodeQL detected code written in JavaScript/TypeScript but could not process any of it. Check the workflow run logs (see https://docs.github.com/en/actions/monitoring-and-troubleshooting-workflows/using-workflow-run-logs). For more information, review our troubleshooting guide at https://gh.io/troubleshooting-code-scanning/no-source-code-seen-during-build .
  Error: Encountered a fatal error while running "/opt/hostedtoolcache/CodeQL/2.22.1/x64/codeql/codeql database finalize --finalize-dataset --threads=2 --ram=6920 /home/runner/work/_temp/codeql_databases/javascript". Exit code was 32 and last log line was: CodeQL detected code written in JavaScript/TypeScript but could not process any of it. Check the workflow run logs (see https://docs.github.com/en/actions/monitoring-and-troubleshooting-workflows/using-workflow-run-logs). For more information, review our troubleshooting guide at https://gh.io/troubleshooting-code-scanning/no-source-code-seen-during-build . See the logs for more details.

Let me know if you need me to rerun it in debug mode or somthing 😉

[lukeramsden]

No JavaScript or TypeScript code found is same error I've been getting - saw first instance of it at Jun 27, 2025, 2:24 PM GMT+1. CodeQL hasn't worked since.

[mbg]

@Th3S4mur41 Thanks for the posting the log so quickly. That's quite a short one! I will check with the relevant team.

[mbg]

@Th3S4mur41 we will need more information about the repo itself. The team has recently made some changes that are intended to exclude generated code from the extraction/analysis. That includes any files contained in the outDir directory specified by a tsconfig.json file and any JavaScript source files that have the same name as a TypeScript source file. Perhaps that is affecting you? Does the repo actually contain a JS/TS codebase?

Anyone else who has the same issue (@lukeramsden), if you are able to share the same information that I asked for in #2955 (comment) or this message, then that would also be helpful.

[Tsingis]

Can check my hobby project https://github.com/Tsingis/cars-data/actions/runs/15959523145. At least some, if not all, of my hobby projects suffer from same issue.

[Th3S4mur41]

@mbg That probably explains it...

The repo is used for building web components and uses storybook for documentation and testing.
The output is configured to the root of the project as you can see in the tsconfig.

{
	"compilerOptions": {
		"target": "es2020",
		"module": "ESNext",
		"lib": ["es2020", "DOM", "DOM.Iterable"],
		"allowJs": true,
		"declaration": true,
		"declarationMap": true,
		"sourceMap": true,
		"inlineSources": true,
		"outDir": ".",
		"rootDir": "./src",
		"strict": true,
		"noUnusedLocals": true,
		"noUnusedParameters": true,
		"noImplicitReturns": true,
		"noFallthroughCasesInSwitch": true,
		"noImplicitAny": true,
		"noImplicitThis": true,
		"moduleResolution": "node",
		"allowSyntheticDefaultImports": true,
		"experimentalDecorators": true,
		"emitDecoratorMetadata": true,
		"forceConsistentCasingInFileNames": true,
		"noImplicitOverride": true,
		"skipLibCheck": true,
		"plugins": [
			{
				"name": "ts-lit-plugin",
				"strict": false
			}
		]
	},
	"include": ["**/*.ts"],
	"exclude": ["**/*.stories.ts", "**/*.template.ts", "**/*.test.ts", "**/*.spec.ts"]
}

Id'd have to double check if this is intentional and still correct though

[mbg]

Thanks both @Tsingis and @Th3S4mur41!

Yes, I can see that the new logic would cause problems in both of these repos. In @Tsingis's, you have outDir set to .. in your app/tsconfig.json and consequently the entire repo gets excluded.

outDir set to . would also cause a problem by excluding everything in that directory and sub-directories.

If you can change outDir to something else that doesn't include the codebase to be analysed, then that should work around the issue for now.

[Tsingis]

@mbg Fixed mine. Thank you. https://github.com/Tsingis/cars-data/actions/runs/15972693152

[mbg]

Also just to confirm, our JS team is looking into how to improve this going forward and they are tracking this issue internally. Once they have a permanent fix, that will be in a future version of the CodeQL CLI.

In the meantime, anyone who is affected by this and is able to do so, can work around the problem by changing outDir.

[ydanneg]

Error: Encountered a fatal error while running "/Users/.../runner-4/_work/_tool/CodeQL/2.22.1/arm64/codeql/codeql database finalize --finalize-dataset --threads=12 --ram=30515 /Users/.../runner-4/_work/_temp/codeql_databases/java". Exit code was 32 and last log line was: CodeQL detected code written in Java/Kotlin but could not process any of it. For more information, review our troubleshooting guide at https://gh.io/troubleshooting-code-scanning/no-source-code-seen-during-build . See the logs for more details.

same happens for our java-kotlin (android) projects.. since last month.. we use

uses: github/codeql-action/init@v3
with:
  queries: security-extended
  languages: java-kotlin
  tools: latest

[ydanneg]

Error: Encountered a fatal error while running "/Users/.../runner-4/_work/_tool/CodeQL/2.22.1/arm64/codeql/codeql database finalize --finalize-dataset --threads=12 --ram=30515 /Users/.../runner-4/_work/_temp/codeql_databases/java". Exit code was 32 and last log line was: CodeQL detected code written in Java/Kotlin but could not process any of it. For more information, review our troubleshooting guide at https://gh.io/troubleshooting-code-scanning/no-source-code-seen-during-build . See the logs for more details.

same happens for our java-kotlin (android) projects.. since last month.. we use

uses: github/codeql-action/init@v3
with:
  queries: security-extended
  languages: java-kotlin
  tools: latest

fixed by adding --no-build-cache to gradle build

[unchris]

We have a similar issue at my company.

background prior to noticing today's new comments (june 30)

Some of our repositories have JS/TS code in a "hidden" folder like .github and .storybook/ usually in the root of the project. We have previously gotten around this problem by setting the following in codeql-config.yaml

paths:
  - ./
  - ./.storybook
  - ./.github 

We are using the advanced setup with a codeql workflow that uses github/codeql-action/init@v3.28.19, codeql-action/autobuild@v3.28.19, github/codeql-action/analyze@v3.28.19. For the most part it's exactly what the basic workflow does - we only use the advanced one so we can integrate it with slight differences in our self-hosted runners, and some private registry auth.

We suspected based on commit history that it might have been something in the bundle for v2.22.1, so we pinned back to v2.22.0 for the init action as below:

tools: https://github.com/github/codeql-action/releases/download/codeql-bundle-v2.22.0/codeql-bundle-linux64.tar.gz

Doing this has worked around the error, but now I see the comment about storybook above and wonder if we have an outDir issue as well?

after recent comments about storybook and generated code

The "base" tsconfig in this project specifies "outDir": "./dist". second tsconfig that extends the base tsconfig specifies "outDir": ""

If I understand the above from @mbg and others, does this mean that because outDir is set to the root folder, we are also automatically excluding the whole repo from processing?