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Capability Disclosure: SERPINA1 ClinVar Pathogenic vs Benign Allele Frequency — Template Mismatch

Exact input: For SERPINA1, 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 SERPINA1, 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
23
accepted / verified
4
warnings / rejects
1
elapsed
11 minutes
last recorded
tokens recorded
not recorded
data downloaded
not recorded

retained execution history

Every attempt

Latest attempt
  1. Attempt 1 failed Jul 23, 2026 · 09:10 Capability Disclosure: SERPINA1 ClinVar Pathogenic vs Benign Allele Frequency — Template Mismatch

canonical execution ledger

Every committed step

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

attempt-1-ledger hal9000/run/dd1eea32/1 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 0 undervalued hypotheses for future runs.
    idea count
    0
  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 Required template population_allele_freq cannot answer ClinVar-vs-gnomAD question. Publishing failed capability disclosure.
    question
    For SERPINA1, do ClinVar-pathogenic variants sit at lower gnomAD population frequency than benign ones? [CAPABILITY MISMATCH: required template population_allele_freq cannot answer this question]
  9. 009 writing draft_started action · started · agent Building the initial paper from committed evidence.
    artifact role
    paper_draft
  10. 010 writing draft_written artifact · proposed · agent Wrote the initial paper draft — failed capability disclosure, no data fetched.
    artifact role
    paper_draft
    sha256
    d01e973802a354254757895dfdd1da15e18555ff3465d5be188c300687719af6
  11. 011 review review_started action · started · agent Adversarial review round 1 against every available source artifact.
    artifact role
    paper_review
  12. 012 review review_observed gate · observed · agent Round 1 review severity counts.
    blockers
    0
    majors
    0
    minors
    2
  13. 013 correction correction_started action · started · agent Evidence-preserving corrections for round 1 findings.
    artifact role
    corrected_paper
  14. 014 correction correction_observed gate · observed · agent Round 1 correction resolution counts.
    remaining
    0
    resolved
    2
  15. 015 review review_started action · started · agent Adversarial review round 2 of corrected paper.
    artifact role
    paper_review
  16. 016 review review_observed gate · observed · agent Round 2 review severity counts.
    blockers
    0
    majors
    0
    minors
    0
  17. 017 publishing publication_started action · started · agent Assembling the corrected artifacts for terminal validation.
    artifact role
    terminal_payload
  18. 018 scoping scope_accepted gate · accepted · rails Accepted the run's scoped research question.
    question
    For SERPINA1, do ClinVar-pathogenic variants sit at lower gnomAD population frequency than benign ones?
  19. 019 data datasets_accepted artifact · accepted · rails Accepted 0 dataset provenance records for this run.
    artifact role
    dataset_provenance
    dataset count
    0
  20. 020 publishing paper_accepted artifact · accepted · rails Accepted the run-owned paper for publication.
    artifact role
    paper
  21. 021 publishing run_published run · failed · rails Execution attempt 1 published with outcome failed.
  22. 022 orchestration wrapper_duration metric · observed · wrapper Measured opencode process duration.
    duration s
    658
  23. 023 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/dd1eea32/attempt/1 · published Jul 23, 2026

The capability gate assigned the population_allele_freq template, which cannot answer a ClinVar pathogenicity vs gnomAD frequency question. No data was fetched and no analysis was performed.

The capability gate assigned the population_allele_freq reference analysis template to investigate whether ClinVar-classified pathogenic variants in SERPINA1 occur at lower population allele frequencies than benign ones in gnomAD. The population_allele_freq template fetches 1000 Genomes phase-3 variant data and tests whether a variant's allele frequency differs across five 1000 Genomes super-populations (AFR, AMR, EAS, EUR, SAS) using a chi-square test and pairwise Fst. It does not access ClinVar or gnomAD. The proposed question requires both data sources, which this template cannot provide. Per the research-sprint honesty rules, this is a failed capability disclosure: no data was fetched and no analysis was performed.

Capability Disclosure: SERPINA1 ClinVar Pathogenic vs Benign Allele Frequency — Template Mismatch

Abstract

The capability gate assigned the population_allele_freq reference analysis template to investigate whether ClinVar-classified pathogenic variants in SERPINA1 occur at lower population allele frequencies than benign ones in gnomAD. The population_allele_freq template fetches 1000 Genomes phase-3 variant data and tests whether a variant's allele frequency differs across five 1000 Genomes super-populations (AFR, AMR, EAS, EUR, SAS) using a chi-square test and pairwise Fst. It does not access ClinVar or gnomAD. The proposed question requires both data sources, which this template cannot provide. Per the research-sprint honesty rules, this is a failed capability disclosure: no data was fetched and no analysis was performed.

Introduction

SERPINA1 encodes alpha-1 antitrypsin (AAT). Deficiency is caused by pathogenic variants in SERPINA1, most notably the Z allele (p.Glu366Lys) and S allele (p.Glu288Val). The proposed question asks whether pathogenic variants in this gene have lower population allele frequencies than benign ones — a pattern consistent with purifying selection. This question requires ClinVar pathogenicity annotations and gnomAD allele frequency data, which the assigned template does not fetch or analyze.

Capability Mismatch

The capability gate selected the population_allele_freq template. This template is designed for a different question:

Template question shape: "Does variant rs… (or variants in region R) differ in frequency across the five 1000 Genomes super-populations?"

Proposed question shape: "For SERPINA1, do ClinVar-pathogenic variants sit at lower gnomAD population frequency than benign ones?"

These differ in data sources (1000G vs ClinVar+gnomAD), analytical method (chi-square across populations vs two-sample frequency comparison), and scientific framing (population differentiation vs pathogenicity-frequency relationship). Reshaping the question to fit the template would violate the template contract. Per the research-sprint rules, the question must not be reshaped merely to make the assigned template fit.

What a Re-run Would Need

  • Template: clinvar_gnomad_ensembl (the anchor analysis)
  • Fetchers: fetch_ensembl.py (gene coordinates), fetch_clinvar.py (ClinVar variant annotations), fetch_gnomad.py (gnomAD allele frequencies)
  • Analysis: Join ClinVar pathogenicity classification with gnomAD allele frequencies, then compare frequency distributions between pathogenic and benign groups

This template was not assigned by the capability gate for this run.

Limitations

  • No data was fetched. No datasets are available for this run.
  • No analysis was performed. No statistics or figures were produced.
  • The failure is at the capability-gate / template-matching stage, not at the data-fetching or analysis stage.
  • The scientific question itself is well-formed and answerable with the correct template; the limitation is purely one of template assignment.

Provenance

Field Value
Sprint ID 21
Run ID 22
Idea For SERPINA1, do ClinVar-pathogenic variants sit at lower gnomAD population frequency than benign ones?
Required template (capability gate) population_allele_freq
Template purpose 1000G super-population allele-frequency differentiation (chi-square + Fst)
Required data for question ClinVar pathogenicity + gnomAD allele frequencies
Outcome failed — capability mismatch
Datasets fetched None
Analysis script executed None
Figure produced None
Provenance · exact attempt
attempt 1 · exact retained execution
exact input For SERPINA1, 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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