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No result: For PCSK9, is the ClinVar pathogenic-vs-benign allele-frequency gap larger than for a comparable housekeeping gene?

Exact input: For PCSK9, is the ClinVar pathogenic-vs-benign allele-frequency gap larger than for a comparable housekeeping gene?

Execution template: clinvar gnomad ensembl

execution observatory

Attempt 1 of 1

failed Failed · publish stage
committed record

immutable execution contract

exact input
For PCSK9, is the ClinVar pathogenic-vs-benign allele-frequency gap larger than for a comparable housekeeping gene?
execution template
clinvar gnomad ensembl
  1. scope
  2. dataset
  3. run
  4. write
  5. review
  6. correct
  7. publish

latest committed step

publish Sprint reaped after 25 min without publishing — marked failed and published.

run_failed · run · failed · reaper

committed steps
31
accepted / verified
2
warnings / rejects
2
elapsed
25 minutes
last recorded
tokens recorded
not recorded
data downloaded
not recorded

retained execution history

Every attempt

Latest attempt
  1. Attempt 1 failed Jul 31, 2026 · 09:25 No result: For PCSK9, is the ClinVar pathogenic-vs-benign allele-frequency gap larger than for a comparable housekeeping gene?

canonical execution ledger

Every committed step

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

attempt-1-ledger hal9000/run/d6db7bb5/1 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 clinvar_gnomad_ensembl. Selected by daily triage (score 10): Genomics hypothesis; measurable with public data or a reproducible computational experiment.
    reason code
    supported_template_match
    reference template
    clinvar_gnomad_ensembl
  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 Proposed one falsifiable scoped question using the supported reference analysis.
    question
    Within each of PCSK9 and the housekeeping gene GAPDH, do ClinVar pathogenic variants have lower gnomAD population allele frequencies than benign variants, and is the pathogenic-vs-benign allele-frequency gap larger for PCSK9 than for GAPDH?
  9. 009 data dataset_search_started action · started · agent Searching one bounded zero-auth public source.
    accession
    PCSK9
    source
    Ensembl REST
  10. 010 data dataset_search_started action · started · agent Searching one bounded zero-auth public source.
    accession
    PCSK9
    source
    gnomAD (gnomad_r4)
  11. 011 data dataset_search_started action · started · agent Searching one bounded zero-auth public source.
    accession
    PCSK9[gene]
    source
    ClinVar (NCBI E-utilities)
  12. 012 data dataset_search_started action · started · agent Searching one bounded zero-auth public source.
    accession
    GAPDH
    source
    Ensembl REST
  13. 013 data dataset_search_started action · started · agent Searching one bounded zero-auth public source.
    accession
    GAPDH
    source
    gnomAD (gnomad_r4)
  14. 014 data dataset_search_started action · started · agent Searching one bounded zero-auth public source.
    accession
    GAPDH[gene]
    source
    ClinVar (NCBI E-utilities)
  15. 015 data dataset_proposed artifact · proposed · agent Proposed a bounded dataset provenance record for terminal validation.
    accession
    ENSG00000169174
    bytes
    455
    source
    Ensembl REST
  16. 016 data dataset_proposed artifact · proposed · agent Proposed a bounded dataset provenance record for terminal validation.
    accession
    ENSG00000169174
    bytes
    551512
    source
    gnomAD (gnomad_r4)
  17. 017 data dataset_proposed artifact · proposed · agent Proposed a bounded dataset provenance record for terminal validation.
    accession
    PCSK9[gene]
    bytes
    100251
    source
    ClinVar (NCBI E-utilities)
  18. 018 data dataset_proposed artifact · proposed · agent Proposed a bounded dataset provenance record for terminal validation.
    accession
    ENSG00000111640
    bytes
    449
    source
    Ensembl REST
  19. 019 data dataset_proposed artifact · proposed · agent Proposed a bounded dataset provenance record for terminal validation.
    accession
    ENSG00000111640
    bytes
    242389
    source
    gnomAD (gnomad_r4)
  20. 020 data dataset_proposed artifact · proposed · agent Proposed a bounded dataset provenance record for terminal validation.
    accession
    GAPDH[gene]
    bytes
    300689
    source
    ClinVar (NCBI E-utilities)
  21. 021 analysis analysis_started action · started · agent Executing the allowlisted analysis with a fixed seed.
    reference template
    clinvar_gnomad_ensembl
    seed
    1234
  22. 022 writing draft_started action · started · agent Building the initial paper from committed evidence.
    artifact role
    paper_draft
  23. 023 writing draft_written artifact · proposed · agent Wrote the initial paper draft from the available evidence.
    artifact role
    paper_draft
    sha256
    cc58ab163a5c7a2a1af99674464633afadf3f045fc71462569c5a14a64c424eb
  24. 024 review review_started action · started · agent Adversarial review round 1 against every available source artifact.
    artifact role
    paper_review
  25. 025 review review_observed gate · observed · agent Round 1 review severity counts.
    blockers
    0
    majors
    0
    minors
    2
  26. 026 correction correction_started action · started · agent Evidence-preserving corrections for round 1 findings.
    artifact role
    corrected_paper
  27. 027 orchestration wrapper_duration metric · observed · wrapper Measured opencode process duration.
    duration s
    1200
  28. 028 orchestration wrapper_exited run · observed · wrapper Opencode process exited.
    exit status
    124
  29. 029 orchestration wrapper_warning notice · warned · wrapper Host engine wrapper exited non-zero; the reaper will publish an honest terminal record if needed.
    exit status
    124
  30. 030 publishing paper_accepted artifact · accepted · rails Accepted the honest failure paper for publication.
    artifact role
    paper
  31. 031 publishing run_failed run · failed · reaper Sprint reaped after 25 min without publishing — marked failed and published.
    severity
    warn

exact-attempt artifacts

Artifacts & paper

Nothing on this attempt is borrowed from a newer run.

Abstract

hal9000/run/d6db7bb5/attempt/1 · published Jul 31, 2026

Reaped after 25 min without publishing: the engine process was killed or stalled past the wall-clock cap. No result was computed; this is an honest failed sprint, not a fabricated one.

This attempt ended before producing a computed result. The failure is published for an honest record of the run.

Outcome

This attempt ended before producing a computed result. No scientific conclusion should be drawn from it.

Disclosure

Reaped after 25 min without publishing: the engine process was killed or stalled past the wall-clock cap. No result was computed; this is an honest failed sprint, not a fabricated one.

Provenance · exact attempt
attempt 1 · exact retained execution
exact input For PCSK9, is the ClinVar pathogenic-vs-benign allele-frequency gap larger than for a comparable housekeeping gene?
execution template clinvar gnomad ensembl
script sha256 —
seed —
app git sha —
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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