Metadata
| Status | done |
|---|---|
| Assigned | agent-971 |
| Agent identity | 3577bc75d6ed4f1947509aa5c086c91ce7c997c7806dab6bf6affac647452647 |
| Created | 2026-05-06T20:26:21.946165590+00:00 |
| Started | 2026-05-06T20:44:04.109340471+00:00 |
| Completed | 2026-05-06T21:07:50.545336668+00:00 |
| Tags | bog-this-week, bog-deck, review-zoom, revision-fanout, eval-scheduled, git-provenance |
| Eval score | 0.96 |
| └ blocking impact | 0.97 |
| └ completeness | 0.98 |
| └ constraint fidelity | 0.85 |
| └ coordination overhead | 0.95 |
| └ correctness | 0.96 |
| └ downstream usability | 0.97 |
| └ efficiency | 0.93 |
| └ intent fidelity | 0.94 |
| └ style adherence | 0.95 |
Description
User review point 6.
Goal: explain why slide 07b seems to show too few subtelomeres and why the tree is small; produce better tree presentation options, including an unrooted tree if defensible.
Requirements:
- Audit current slide 07b tree asset and source scripts/data.
- Determine whether all 41 expected arms are present and, if not, why not. If all are present but unreadable, say that directly.
- Generate or specify a larger rooted tree layout and an unrooted NJ tree option from the arm-level distance matrix.
- Label/highlight named clades consistently with slide 09 communities and abstract vocabulary.
- Do not edit deck source; final integration will render.
Deliverables:
- Markdown audit: all subtelomeres present/missing, data source, tree algorithm, recommendation.
- Candidate rooted and/or unrooted tree asset(s) under slides/v2-review-zoom/_revision_assets/07b_tree_options/.
Depends on
Required by
Log
- 2026-05-06T20:26:21.917997001+00:00 Task paused
- 2026-05-06T20:28:35.239683864+00:00 Task published
- 2026-05-06T20:44:04.109344288+00:00 Spawned by coordinator --executor codex --model gpt-5.5
- 2026-05-06T20:44:30.555420642+00:00 Starting audit of slide 07b tree sources and arm-level matrix; no unread messages at start.
- 2026-05-06T20:53:50.596243050+00:00 Audited sources: current s07b PNG is the upstream rooted NJ render from paper_prep/figures/nj_tree_arms; the matrix and Leiden assignment tables contain 41 arms, with seven zero-signal arms absent by construction.
- 2026-05-06T21:05:35.952228055+00:00 Generated 07b tree options and audit tables under slides/v2-review-zoom/_revision_assets/07b_tree_options; rooted and unrooted NJ assets use the canonical 41x41 arm-level distance matrix.
- 2026-05-06T21:06:18.106305488+00:00 Validated: README re-read against task requirements; arm_presence.tsv covers 48-arm presence/missing audit; matrix_audit.tsv confirms 41x41 input; clade_recovery.tsv confirms all six named slide09/abstract clades are monophyletic; generated PNG dimensions verified; git diff --check passes.
- 2026-05-06T21:07:15.715134627+00:00 Committed: ba3c52d — pushed to origin/wg/agent-971/review-zoom-07b-tree-complete-unrooted
- 2026-05-06T21:07:50.545347849+00:00 Task pending eval (agent reported done; awaiting `.evaluate-*` to score)
- 2026-05-06T21:13:27.498124124+00:00 PendingEval → Done (evaluator passed; downstream unblocks)