Fatal Error: Tuple [...] has incorrect number of columns in C# CodeQL

[Sella-GH]

While running a scheduled CodeQL run tonight it started to fail when trying to evaluate the queries.

Following log files being shown with the error (and some debug lines)

2025-01-21T13:10:06.2758939Z Starting evaluation of codeql/csharp-queries/API Abuse/CallToGCCollect.ql.
2025-01-21T13:10:06.2768064Z Starting evaluation of codeql/csharp-queries/API Abuse/CallToObsoleteMethod.ql.
2025-01-21T13:10:06.2769474Z Starting evaluation of codeql/csharp-queries/API Abuse/ClassDoesNotImplementEquals.ql.
2025-01-21T13:10:06.2797175Z Starting evaluation of codeql/csharp-queries/API Abuse/ClassImplementsICloneable.ql.
2025-01-21T13:10:06.2817513Z Starting evaluation of codeql/csharp-queries/API Abuse/DisposeNotCalledOnException.ql.
2025-01-21T13:10:06.2819123Z Starting evaluation of codeql/csharp-queries/API Abuse/FormatInvalid.ql.
2025-01-21T13:10:06.2827921Z Starting evaluation of codeql/csharp-queries/API Abuse/InconsistentEqualsGetHashCode.ql.
2025-01-21T13:10:10.0185233Z [1/194 eval 3.7s] Evaluation done; writing results to codeql/csharp-queries/API Abuse/CallToGCCollect.bqrs.
2025-01-21T13:10:10.4471096Z [2/194 eval 4.2s] Evaluation done; writing results to codeql/csharp-queries/API Abuse/CallToObsoleteMethod.bqrs.
2025-01-21T13:10:10.8126847Z [3/194 eval 4.5s] Evaluation done; writing results to codeql/csharp-queries/API Abuse/ClassImplementsICloneable.bqrs.
2025-01-21T13:10:12.8573439Z Starting evaluation of codeql/csharp-queries/API Abuse/IncorrectCompareToSignature.ql.
2025-01-21T13:10:12.8738760Z Starting evaluation of codeql/csharp-queries/API Abuse/IncorrectEqualsSignature.ql.
2025-01-21T13:10:14.4805367Z [4/194 eval 1.6s] Evaluation done; writing results to codeql/csharp-queries/API Abuse/IncorrectCompareToSignature.bqrs.
2025-01-21T13:10:14.4836806Z Starting evaluation of codeql/csharp-queries/API Abuse/NoDisposeCallOnLocalIDisposable.ql.
2025-01-21T13:10:14.6180164Z A fatal error occurred: A tuple in a data extension for the extensible predicate 'sourceModel' has an incorrect number of columns. Expected 10, but was 9.
2025-01-21T13:10:15.6847658Z ##[error]Error running analysis for csharp: Encountered a fatal error while running "/opt/hostedtoolcache/CodeQL/2.20.1/x64/codeql/codeql database run-queries --ram=14567 --threads=4 /home/runner/work/_temp/codeql_databases/csharp --expect-discarded-cache --min-disk-free=1024 -v --intra-layer-parallelism". Exit code was 2 and error was: A fatal error occurred: A tuple in a data extension for the extensible predicate 'sourceModel' has an incorrect number of columns. Expected 10, but was 9. See the logs for more details.
2025-01-21T13:10:15.6894812Z ##[debug]Sending status report: {"action_name":"finish","action_oid":"unknown","action_ref":"b6a472f63d85b9c78a3ac5e89422239fc15e9b3c","action_started_at":"2025-01-21T13:09:38.538Z","action_version":"3.28.1","analysis_key":".github/workflows/codeql.yml:analyze","build_mode":"manual","commit_oid":"849ce79dee3ef79ee7e50a21d03913f98a4b4972","first_party_analysis":true,"job_name":"analyze","job_run_uuid":"00b5dc4b-9b9b-4048-99c1-aedbb8b7b3aa","ref":"refs/heads/main","runner_os":"Linux","started_at":"2025-01-21T13:07:41.332Z","status":"failure","steady_state_default_setup":false,"testing_environment":"","workflow_name":"CodeQL","workflow_run_attempt":2,"workflow_run_id":12887566233,"actions_event_name":"push","languages":"csharp","runner_available_disk_space_bytes":21452361728,"runner_total_disk_space_bytes":77851254784,"cause":"Encountered a fatal error while running \"/opt/hostedtoolcache/CodeQL/2.20.1/x64/codeql/codeql database run-queries --ram=14567 --threads=4 /home/runner/work/_temp/codeql_databases/csharp --expect-discarded-cache --min-disk-free=1024 -v --intra-layer-parallelism\". Exit code was 2 and error was: A fatal error occurred: A tuple in a data extension for the extensible predicate 'sourceModel' has an incorrect number of columns. Expected 10, but was 9. See the logs for more details.","exception":"Error: Encountered a fatal error while running \"/opt/hostedtoolcache/CodeQL/2.20.1/x64/codeql/codeql database run-queries --ram=14567 --threads=4 /home/runner/work/_temp/codeql_databases/csharp --expect-discarded-cache --min-disk-free=1024 -v --intra-layer-parallelism\". Exit code was 2 and error was: A fatal error occurred: A tuple in a data extension for the extensible predicate 'sourceModel' has an incorrect number of columns. Expected 10, but was 9. See the logs for more details.\n    at runCli (/home/runner/work/_actions/github/codeql-action/b6a472f63d85b9c78a3ac5e89422239fc15e9b3c/lib/codeql.js:763:63)\n    at process.processTicksAndRejections (node:internal/process/task_queues:95:5)\n    at async Object.databaseRunQueries (/home/runner/work/_actions/github/codeql-action/b6a472f63d85b9c78a3ac5e89422239fc15e9b3c/lib/codeql.js:478:13)\n    at async runQueries (/home/runner/work/_actions/github/codeql-action/b6a472f63d85b9c78a3ac5e89422239fc15e9b3c/lib/analyze.js:343:13)\n    at async run (/home/runner/work/_actions/github/codeql-action/b6a472f63d85b9c78a3ac5e89422239fc15e9b3c/lib/analyze-action.js:196:24)\n    at async runWrapper (/home/runner/work/_actions/github/codeql-action/b6a472f63d85b9c78a3ac5e89422239fc15e9b3c/lib/analyze-action.js:268:9)","completed_at":"2025-01-21T13:10:15.687Z","matrix_vars":"{\n  \"language\": \"csharp\",\n  \"build-mode\": \"manual\"\n}","runner_arch":"X64","runner_os_release":"6.5.0-1025-azure","codeql_version":"2.20.1","runner_image_version":"20250120.2.0","analyze_failure_language":"csharp","scanned_language_extraction_duration_ms":3,"trap_import_duration_ms":11845}
2025-01-21T13:10:15.8313927Z ##[debug]Node Action run completed with exit code 1
2025-01-21T13:10:15.8316092Z ##[debug]CODEQL_ACTION_FEATURE_MULTI_LANGUAGE='false'
2025-01-21T13:10:15.8316540Z ##[debug]CODEQL_ACTION_FEATURE_SANDWICH='false'
2025-01-21T13:10:15.8317235Z ##[debug]CODEQL_ACTION_FEATURE_SARIF_COMBINE='true'
2025-01-21T13:10:15.8317632Z ##[debug]CODEQL_ACTION_FEATURE_WILL_UPLOAD='true'
2025-01-21T13:10:15.8317993Z ##[debug]CODEQL_ACTION_VERSION='3.28.1'
2025-01-21T13:10:15.8318456Z ##[debug]CODEQL_ACTION_SARIF_RESULTS_OUTPUT_DIR='sarif-results'
2025-01-21T13:10:15.8319120Z ##[debug]CODEQL_ACTION_JOB_STATUS='JOB_STATUS_FAILURE'
2025-01-21T13:10:15.8323168Z ##[debug]Save intra-action state persisted_inputs = [["INPUT_CATEGORY","/language:csharp"],["INPUT_OUTPUT","sarif-results"],["INPUT_UPLOAD","failure-only"],["INPUT_CHECK_NAME",""],["INPUT_CLEANUP-LEVEL","brutal"],["INPUT_RAM",""],["INPUT_ADD-SNIPPETS","false"],["INPUT_SKIP-QUERIES","false"],["INPUT_THREADS",""],["INPUT_CHECKOUT_PATH","/home/runner/work/AzzyBot/AzzyBot"],["INPUT_REF",""],["INPUT_SHA",""],["INPUT_UPLOAD-DATABASE","true"],["INPUT_WAIT-FOR-PROCESSING","true"],["INPUT_TOKEN","***"],["INPUT_MATRIX","{\n  \"language\": \"csharp\",\n  \"build-mode\": \"manual\"\n}"],["INPUT_EXPECT-ERROR","false"]]
2025-01-21T13:10:15.8328322Z ##[debug]Finishing: Perform CodeQL Analysis

My CodeQL configuration:

https://github.com/Sella-GH/AzzyBot/blob/main/.github/workflows/codeql.yml

[aeisenberg]

Thanks for reporting. One of our engineers will be looking at this tomorrow.

[hvitved]

My guess is that somehow an old CLI, which predates support for auto-populating QlBuiltins::ExtensionId columns, is being used with a version of the QL code that requires it.

[aeisenberg]

I don't think that's the case. Here's a failing workflow that is using 2.20.1 (the most recent release).

But I do think there is some mismatch in there. Perhaps the githubsecuritylab/codeql-csharp-queries query pack, is incompatible because it was compiled under an older CLI?

[Sella-GH]

I already thought it could be that one but that query pack received an update tonight... maybe that's why it's failing.

Edit: According to the repo's source it seems they're using the newest CLI version available.
https://github.com/GitHubSecurityLab/CodeQL-Community-Packs/blob/main/.github/workflows/publish.yml#L9

[Sella-GH]

Okay I disabled the extension packs and now it works fine again. Seems like this was the cause of the issue.

I am creating an issue in the GitHubSecurityLab Repo and reference this one. Looks like something's wrong there.

[aeisenberg]

Thanks for verifying and following up.