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MCM6 ClinVar pathogenic-vs-benign allele-frequency gap: capability mismatch, no computed result

Exact input: For MCM6, is the ClinVar pathogenic-vs-benign allele-frequency gap larger than for a comparable housekeeping gene?

Execution template: ancient selection trajectory

execution observatory

Attempt 1 of 1

failed Failed · publish stage
committed record

immutable execution contract

exact input
For MCM6, is the ClinVar pathogenic-vs-benign allele-frequency gap larger than for a comparable housekeeping gene?
execution template
ancient selection trajectory
  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
10 minutes
last recorded
tokens recorded
not recorded
data downloaded
not recorded

retained execution history

Every attempt

Latest attempt
  1. Attempt 1 failed Aug 2, 2026 · 09:09 MCM6 ClinVar pathogenic-vs-benign allele-frequency gap: capability mismatch, no computed result

canonical execution ledger

Every committed step

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

attempt-1-ledger hal9000/run/02da0773/1 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 ancient_selection_trajectory. Selected by daily triage (score 10): Genomics hypothesis; measurable with public data or a reproducible computational experiment.
    reason code
    supported_template_match
    reference template
    ancient_selection_trajectory
  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 Scoped: no compatible allowlisted analysis exists for this idea under the required template; publishing an honest failed capability disclosure.
    question
    For MCM6, is the ClinVar pathogenic-vs-benign allele-frequency gap larger than for a comparable housekeeping gene?
  9. 009 writing draft_started action · started · agent Building the initial failed-capability paper from the scoping evidence.
    artifact role
    paper_draft
  10. 010 writing draft_written artifact · proposed · agent Wrote the initial failed-capability paper draft.
    artifact role
    paper_draft
    sha256
    1188dd7a517de725aa9a67548a8e313291d3db96001c1755e719046d7ef378bc
  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
    1
  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
    1
  15. 015 review review_started action · started · agent Adversarial review round 2 of the corrected paper against every available source artifact.
    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 failed-capability 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 MCM6, is the ClinVar pathogenic-vs-benign allele-frequency gap larger than for a comparable housekeeping gene?
  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
    579
  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/02da0773/attempt/1 · published Aug 2, 2026 · No computed statistic — failed capability disclosure (required template cannot answer the scoped question).

No computed statistic — failed capability disclosure (required template cannot answer the scoped question).

Capability mismatch: the persisted execution contract requires reference_template ancient_selection_trajectory (single-locus ancient-DNA allele-frequency trend on the Allen Ancient DNA Resource). The scoped question — comparing the ClinVar pathogenic-vs-benign allele-frequency gap between MCM6 and a comparable housekeeping gene — requires the clinvar_gnomad_ensembl analysis (ClinVar classifications + gnomAD population frequencies for two genes). The required template has no mechanism to classify variants as pathogenic/benign, no mechanism to fetch population allele frequencies, and is a single-locus scan. The engine rejects any other reference_template. Per the honesty rules the run publishes an explicit failed disclosure instead of reshaping the idea. No dataset was fetched (download_bytes = 0) and no analysis ran (no statistic, no figure).

This sprint was scoped from the idea "For MCM6, is the ClinVar pathogenic-vs-benign
allele-frequency gap larger than for a comparable housekeeping gene?" The question
is a two-gene ClinVar × gnomAD comparison: it requires variant-level clinical
classification (pathogenic vs. benign) joined to population allele frequencies for
two genes. That is the domain of the clinvar_gnomad_ensembl allowlisted
reference analysis. The capability gate for this exact run persisted the required
template ancient_selection_trajectory, a single-locus ancient-DNA allele-frequency
trend analysis on the Allen Ancient DNA Resource (AADR), which measures how one
known selected allele (e.g. LCT/MCM6 rs4988235) rose or fell over millennia. That
template cannot compute a ClinVar pathogenic-vs-benign allele-frequency gap for one
gene, let alone compare the gap between MCM6 and a housekeeping gene. The engine
rejects substitution of any other reference_template, so no allowlisted analysis
can honestly answer the scoped question in this run. Per the sprint's honesty rules,
we publish an explicit failed capability disclosure instead of reshaping the idea or
running an unrelated analysis. No dataset was fetched and no statistic was computed.

MCM6 ClinVar pathogenic-vs-benign allele-frequency gap: capability mismatch, no computed result

Abstract

This sprint was scoped from the idea "For MCM6, is the ClinVar pathogenic-vs-benign
allele-frequency gap larger than for a comparable housekeeping gene?" The question
is a two-gene ClinVar × gnomAD comparison: it requires variant-level clinical
classification (pathogenic vs. benign) joined to population allele frequencies for
two genes. That is the domain of the clinvar_gnomad_ensembl allowlisted
reference analysis. The capability gate for this exact run persisted the required
template ancient_selection_trajectory, a single-locus ancient-DNA allele-frequency
trend analysis on the Allen Ancient DNA Resource (AADR), which measures how one
known selected allele (e.g. LCT/MCM6 rs4988235) rose or fell over millennia. That
template cannot compute a ClinVar pathogenic-vs-benign allele-frequency gap for one
gene, let alone compare the gap between MCM6 and a housekeeping gene. The engine
rejects substitution of any other reference_template, so no allowlisted analysis
can honestly answer the scoped question in this run. Per the sprint's honesty rules,
we publish an explicit failed capability disclosure instead of reshaping the idea or
running an unrelated analysis. No dataset was fetched and no statistic was computed.

Scoped question

For MCM6, is the ClinVar pathogenic-vs-benign allele-frequency gap larger than for
a comparable housekeeping gene?

Capability decision

  • Required reference template (persisted): ancient_selection_trajectory
  • Template question shape: "Did allele rs… rise/fall over time in ancient DNA?" — a single-locus OLS of ALT-allele dosage on sample date (years BP) using the Allen Ancient DNA Resource. Fetcher: fetch_aadr.py --locus lct|slc24a5|….
  • Template inputs: AADR genotype calls for one locus; no ClinVar variant classifications and no gnomAD population frequencies.
  • What the scoped question needs: ClinVar pathogenic/benign classifications plus population allele frequencies, joined per variant, for two genes (MCM6 and a comparable housekeeping gene), so the pathogenic-vs-benign allele-frequency gap can be estimated for each and compared.

These requirements are disjoint. ancient_selection_trajectory has no mechanism to
classify variants as pathogenic or benign, no mechanism to fetch population allele
frequencies, and is explicitly a single-locus scan — it cannot compare two genes.
The allowlisted analysis that does fit the question (clinvar_gnomad_ensembl) was
not selected by the capability gate, and the ingest boundary rejects a
reference_template that differs from the persisted execution contract.

Methods

Because the required template cannot honestly answer the scoped question, the run
stopped at the scoping stage. In line with the sprint's failed-outcome protocol:

  • No dataset was fetched (nothing compatible with the question was needed; we did not fetch unrelated AADR data merely to populate the ledger).
  • No analysis was executed, so no stats.json and no figure.png exist.
  • download_bytes is therefore 0 and analysis.duration_s is absent.
  • The paper records this capability mismatch and what a re-run would need, rather than fabricating a number or reshaping the idea to force the template to fit.

Result

Outcome: failed (capability mismatch). No computed statistic exists for this
run. No claim about the MCM6 ClinVar pathogenic-vs-benign allele-frequency gap
being larger or smaller than that of a housekeeping gene is made, because no such
measurement was performed. Any number presented here as the answer would be a
fabrication, which this sprint's manifesto forbids.

Limitations and disclosure

  • The required template ancient_selection_trajectory cannot measure a ClinVar pathogenic-vs-benign allele-frequency gap; this is a capability mismatch of the persisted execution contract, not a null scientific result.
  • No dataset provenance rows exist because nothing was fetched; no analysis script exists because nothing was run. These absences are intentional and disclosed.
  • A future run that can honestly answer the question needs the capability gate to persist the clinvar_gnomad_ensembl anchor for both MCM6 and a comparable housekeeping gene (e.g. a stably expressed gene with comparable ClinVar annotation volume), then compare the two genes' pathogenic-vs-benign allele-frequency gaps.
  • The idea as written presupposes MCM6 is "comparable" to a housekeeping gene; even in a correctly-gated run, a well-defined housekeeping-gene control and a pre-registered comparison metric would be required for the comparison to be interpretable.

Provenance

No dataset was fetched during this run, so the dataset provenance table has zero
rows (there is no source, accession, access URL, or region slice to record):

Dataset Source Accession Access URL Region slice
(none) — — — —
  • Analysis: not run (capability mismatch).
  • Seed: not applicable.
  • Figure: none.
  • download_bytes is 0 — this is the measured total, since nothing was fetched.
Provenance · exact attempt
attempt 1 · exact retained execution
exact input For MCM6, is the ClinVar pathogenic-vs-benign allele-frequency gap larger than for a comparable housekeeping gene?
execution template ancient selection trajectory
script sha256 —
seed —
app git sha 90235e290363ee8922771b653ade6ffe7248ff2f
corrections none

No analysis script — sprint stopped before authoring one.

deterministic re-runs of this exact attempt

Reproduction attempts

Executor health and scientific verdict are separate. Public-safe summaries only; leases and raw process output are never shown.

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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