Metadata
| Status | done |
|---|---|
| Assigned | agent-632 |
| Agent identity | 3577bc75d6ed4f1947509aa5c086c91ce7c997c7806dab6bf6affac647452647 |
| Created | 2026-05-04T22:32:54.071506452+00:00 |
| Started | 2026-05-04T22:43:09.855096025+00:00 |
| Completed | 2026-05-04T23:44:14.490885743+00:00 |
| Tags | paper-prep,survey, eval-scheduled |
| Tokens | 171041 in / 32 out |
| Eval score | 0.88 |
| └ blocking impact | 0.80 |
| └ completeness | 0.92 |
| └ coordination overhead | 0.85 |
| └ correctness | 0.95 |
| └ downstream usability | 0.88 |
| └ efficiency | 0.70 |
| └ intent fidelity | 0.65 |
| └ style adherence | 0.90 |
Description
INPUT: end-to-end-report/report/03_gene_enrichment.md (read fully). CONTEXT: Nature manuscript + 15-min talk on subtelomeric sequence sharing; this task surveys ONE section. Note: the repo has many gene-enrichment artifacts (copy_number_enrichment_*.csv, *.md syntheses) — cross-reference paths from the section text. TASK: Extract: (1) Key findings with metrics (top hit p-values, gene counts, biotype %s); (2) Existing figures referenced (paths); (3) Existing CSVs/tables (paths); (4) Methods (note copy-number-aware ORA work); (5) Gaps for figure (re)generation; (6) Suggested figures main+SI with captions, marking produced-vs-todo; (7) Talk slide takeaways. OUTPUT: paper_prep/surveys/SURVEY_03_gene_enrichment.md (7 numbered sections). ACCEPTANCE: File exists, all 7 sections present, concrete paths cited.
Depends on
Required by
Log
- 2026-05-04T22:32:54.057992626+00:00 Task paused
- 2026-05-04T22:41:53.222594690+00:00 Task published
- 2026-05-04T22:42:33.953671839+00:00 Lightweight assignment: agent=random-agent-3577bc75 (3577bc75), exec_mode=full, context_scope=task, reason=Documenter role fits survey extraction task; tradeoff 'verify-against-code-not-just-docs' ensures concrete path references required by acceptance criteria.
- 2026-05-04T22:43:09.855099631+00:00 Spawned by coordinator --executor claude --model opus
- 2026-05-04T22:43:40.884349385+00:00 Starting survey of gene enrichment section
- 2026-05-04T22:45:25.508606323+00:00 Inventory complete: section narrates arm-level enrichment but only sequence-level plots have been rendered; arm-level TSVs exist without plots.
- 2026-05-04T22:50:51.286143048+00:00 Validated: all 7 sections present; concrete paths cited; key gap = arm-level plots not rendered.
- 2026-05-04T23:17:33.202242220+00:00 Survey file produced; commit blocked by heavy concurrent git contention from sibling squash-merges. Retrying.
- 2026-05-04T23:31:35.841987897+00:00 Survey re-written (3rd time after I/O storms wiped earlier copies). File has 259 lines, all 7 sections present.
- 2026-05-04T23:34:17.899045770+00:00 Validated: file intact (259 lines, 26253 bytes), all 7 numbered sections present, paths cited (arm-level enrichment dir, sequence-level enrichment dir, scripts, repo-root copy-aware artifacts). Acceptance criteria met.
- 2026-05-04T23:34:17.982147338+00:00 INFRASTRUCTURE BLOCKER: shared moosefs git tree has been in sustained livelock since ~22:50 UTC. HEAD at 67da9c4; no commits (mine or 5 sibling squash-merges) have landed. moosefs returns persistent Input/output errors on .git writes; orchestrator squash-merge processes for SURVEY_01/02/04/05/06 are also stuck. File deliverable is on disk and recorded as wg artifact for eval verification.
- 2026-05-04T23:44:11.919625288+00:00 Final state: file deliverable on disk (26253 bytes, 259 lines, 7 sections), wg artifact registered. git commit/push blocked by 50+ min sustained livelock on shared moosefs .git tree affecting all sibling agents (HEAD still 67da9c4; sibling surveys 01/02/04/05/06 also blocked). Marking done — file deliverable meets acceptance criteria; commit can be landed by orchestrator when filesystem recovers.
- 2026-05-04T23:44:14.490900030+00:00 Task pending eval (agent reported done; awaiting `.evaluate-*` to score)
- 2026-05-04T23:48:21.590404524+00:00 PendingEval → Done (evaluator passed; downstream unblocks)