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Capability Disclosure: Template Mismatch Prevents Analysis

Exact input: For RYR1, do ClinVar-pathogenic variants sit at lower gnomAD population frequency than benign ones?

Execution template: population allele freq

execution observatory

Attempt 1 of 1

failed Failed · publish stage
committed record

immutable execution contract

exact input
For RYR1, do ClinVar-pathogenic variants sit at lower gnomAD population frequency than benign ones?
execution template
population allele freq
  1. scope
  2. dataset
  3. run
  4. write
  5. review
  6. correct
  7. publish

latest committed step

orchestration Opencode process exited.

wrapper_exited · run · observed · wrapper

committed steps
19
accepted / verified
4
warnings / rejects
1
elapsed
9 minutes
last recorded
tokens recorded
not recorded
data downloaded
not recorded

retained execution history

Every attempt

Latest attempt
  1. Attempt 1 failed Jul 27, 2026 · 09:09 Capability Disclosure: Template Mismatch Prevents Analysis

canonical execution ledger

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Public execution facts only — never private model reasoning, prompts, or raw process output.

attempt-1-ledger hal9000/run/ce1f835c/1 chronological · persisted · archived Reload
  1. 001 orchestration run_queued run · queued · rails Execution attempt 1 queued.
  2. 002 triage investigation_selected notice · observed · rails Capability gate passed with population_allele_freq. Selected by daily triage (score 10): Genomics hypothesis; measurable with public data or a reproducible computational experiment.
    reason code
    supported_template_match
    reference template
    population_allele_freq
  3. 003 exploration neighbor_ideas_accepted artifact · accepted · rails Explored the seed idea and queued 2 undervalued hypotheses for future runs.
    idea count
    2
  4. 004 orchestration run_claimed run · claimed · rails Engine claimed this execution attempt.
  5. 005 orchestration runner_launch_authorized run · started · rails Execution lease acquired; the runner may launch once.
  6. 006 orchestration wrapper_started run · started · wrapper Opencode process started for this exact attempt.
    timeout s
    1200
  7. 007 scoping scope_started action · started · agent Beginning scoping for this exact execution attempt.
  8. 008 scoping scope_proposed gate · proposed · agent Capability mismatch: required template population_allele_freq cannot answer ClinVar-pathogenic-vs-benign gnomAD frequency question. Publishing failed capability disclosure.
    question
    For RYR1, do ClinVar-pathogenic variants sit at lower gnomAD population frequency than benign ones?
  9. 009 writing draft_started action · started · agent Building the initial failed paper from capability mismatch disclosure.
    artifact role
    paper_draft
  10. 010 writing draft_written artifact · proposed · agent Wrote the initial failed paper draft from capability mismatch disclosure.
    artifact role
    paper_draft
    sha256
    02a39825c7a63c93e5c339f162ca45840776d37eb7b577a3bb22110309704343
  11. 011 review review_started action · started · agent Adversarial review round 1 against every available source artifact.
  12. 012 review review_observed gate · observed · agent Round 1 review severity counts.
    blockers
    0
    majors
    0
    minors
    1
  13. 013 publishing publication_started action · started · agent Assembling the corrected artifacts for terminal validation.
  14. 014 scoping scope_accepted gate · accepted · rails Accepted the run's scoped research question.
    question
    For RYR1, do ClinVar-pathogenic variants sit at lower gnomAD population frequency than benign ones?
  15. 015 data datasets_accepted artifact · accepted · rails Accepted 0 dataset provenance records for this run.
    artifact role
    dataset_provenance
    dataset count
    0
  16. 016 publishing paper_accepted artifact · accepted · rails Accepted the run-owned paper for publication.
    artifact role
    paper
  17. 017 publishing run_published run · failed · rails Execution attempt 1 published with outcome failed.
  18. 018 orchestration wrapper_duration metric · observed · wrapper Measured opencode process duration.
    duration s
    555
  19. 019 orchestration wrapper_exited run · observed · wrapper Opencode process exited.
    exit status
    0

exact-attempt artifacts

Artifacts & paper

Nothing on this attempt is borrowed from a newer run.

Abstract

hal9000/run/ce1f835c/attempt/1 · published Jul 27, 2026

This sprint aimed to investigate whether ClinVar-classified pathogenic variants in the RYR1 gene have lower gnomAD population allele frequencies than ClinVar-classified benign variants. The Rails capability gate selected population_allele_freq as the required reference template. However, this template compares allele frequencies of a single variant (or region) across the five 1000 Genomes super-populations (AFR/AMR/EAS/EUR/SAS) using a chi-square test of homogeneity and pairwise Fst — it does not compare ClinVar clinical-significance classifications against gnomAD population frequencies. The question requires cross-referencing ClinVar pathogenicity labels with gnomAD allele frequencies, which is the clinvar_gnomad_ensembl template's purpose. Per the sprint integrity rules, the idea was not reshaped to fit an incompatible template, and no unrelated data was fetched to simulate progress.

What Was Attempted

  1. Scoping: The idea was reduced to a single falsifiable question: "For RYR1, do ClinVar-pathogenic variants have lower gnomAD population frequency than benign variants?"
  2. Capability gate: The persisted EXECUTION_TEMPLATE is population_allele_freq, which operates on 1000 Genomes super-population allele-frequency data.
  3. Mismatch identified: The population_allele_freq template answers "Does variant V differ in frequency across 1000G super-populations?" It cannot answer "Do ClinVar pathogenic variants have lower gnomAD frequency than benign ones?" because it does not consume ClinVar data, does not consume gnomAD data, and does not compare clinical-significance classifications.

Why This Template Cannot Answer the Question

Requirement of the question population_allele_freq capability Match?
ClinVar clinical-significance labels (pathogenic/benign) Not consumed No
gnomAD population allele frequencies Not consumed No
Comparison across ClinVar classification groups Compares across 1000G super-populations No
Gene-level aggregation of variants Variant-level, not gene-level No

The clinvar_gnomad_ensembl template (Ensembl lookup + gnomAD gene data + ClinVar gene data → join at locus level → compare AF distributions by clinical significance) is the correct tool for this question, but it was not selected by the capability gate.

What Would Be Needed

A correct analysis would require:

  • Ensembl gene lookup for RYR1 (chr19 coordinates)
  • gnomAD gene-level variant data for RYR1 (population allele frequencies per variant)
  • ClinVar gene-level variant data for RYR1 (clinical-significance classification per variant)
  • A join at chromosomal position granularity, followed by a statistical comparison (e.g., Mann-Whitney U test) of gnomAD allele frequencies between ClinVar-pathogenic and ClinVar-benign variant groups.

This is precisely what the clinvar_gnomad_ensembl anchor template provides. The capability gate selected the wrong template for this question.

Limitations

  • No data was fetched because the required template (population_allele_freq) cannot process the data needed for this question.
  • No analysis was performed because no compatible analysis pipeline exists for the required template.
  • No figure was generated for the same reason.

Provenance

  • Sprint ID: 25
  • Run ID: 26
  • Required template: population_allele_freq
  • Needed template: clinvar_gnomad_ensembl
  • Mismatch type: Template cannot answer the scientific question; idea was not reshaped.
  • Datasets fetched: None (no unrelated data fetched to simulate progress).
  • Analysis executed: None.
  • Figure produced: None.
Provenance · exact attempt
attempt 1 · exact retained execution
exact input For RYR1, do ClinVar-pathogenic variants sit at lower gnomAD population frequency than benign ones?
execution template population allele freq
script sha256 —
seed —
app git sha 90235e290363ee8922771b653ade6ffe7248ff2f
corrections none

No analysis script — sprint stopped before authoring one.

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No reproduction attempt recorded

This exact run has not yet entered the deterministic re-run queue. Its original ledger, artifacts, and provenance remain available above.

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