Metadata
| Status | done |
|---|---|
| Assigned | agent-2749 |
| Agent identity | 46f6237a65ec4f1002c4d3fb201dc8633638d0947c276be7008c227e1051ba5e |
| Created | 2026-06-25T16:24:29.164501347+00:00 |
| Started | 2026-06-25T16:26:45.839254393+00:00 |
| Completed | 2026-06-25T16:35:49.193329525+00:00 |
| Tags | eval-scheduled |
| Eval score | 0.87 |
| └ blocking impact | 0.90 |
| └ completeness | 0.86 |
| └ constraint fidelity | 0.85 |
| └ coordination overhead | 0.76 |
| └ correctness | 0.89 |
| └ downstream usability | 0.91 |
| └ efficiency | 0.83 |
| └ style adherence | 0.88 |
Description
Evaluate a safer non-graph alternative for whole-genome-style Fig5 support. Use 2 kb query-grid windows around the candidate and control regions, then measure target support directly by pairwise alignment / match-distance or IMPG-style similarity, avoiding seqwish/ODGI graph construction. Compare WFMASH/SweepGA-filtered evidence to direct similarity summaries in query space; report whether PAN027 chr9q and PAN028 chr9q recover chr3q support and whether PAR/acros controls behave as expected. Use Slurm for heavy compute; do not run on the head node. Produce a concise report and TSV outputs under paper_prep/_brainstorming/fig5_2kb_direct_similarity_pilot/.
Depends on
Required by
Log
- 2026-06-25T16:25:49.282311211+00:00 Lightweight assignment: agent=random-agent-46f6237a (46f6237a), exec_mode=full, context_scope=task, reason=Pipeline Operator best matches the compute-heavy, Slurm-backed analysis and output generation work with concrete execution over abstraction.
- 2026-06-25T16:26:29.670060588+00:00 Refined design from user: do not require graph construction. Use existing whole-genome alignments as the backing evidence for an IMPG-like/query-space similarity summary. Prefer raw/many:many WFMASH and SweepGA/FastGA f32 PAFs, plus optionally the existing 2kb query-grid 1:1 filtered PAFs as conservative sensitivity. Slice/query by native candidate/control intervals, summarize best/all target chromosome support per 2kb query bin using identity/match-distance/aligned bp, and compare chr9q->chr3q, PAR, and acrocentric controls. Avoid launching seqwish/ODGI unless explicitly requested later.
- 2026-06-25T16:26:45.839259603+00:00 Spawned by coordinator --executor codex --model gpt-5.5
- 2026-06-25T16:27:06.424521720+00:00 Starting direct-similarity pilot; inspecting candidate windows, manifests, and available alignment evidence.
- 2026-06-25T16:32:00.735980043+00:00 Validated: reran direct-similarity pilot and py_compile; outputs generated under paper_prep/_brainstorming/fig5_2kb_direct_similarity_pilot/.
- 2026-06-25T16:34:23.484049467+00:00 Committed: 07df829 — fig5 2kb direct similarity pilot outputs and report.
- 2026-06-25T16:35:07.754481554+00:00 Pushed branch wg/agent-2749/fig5-2kb-direct-similarity-pilot to origin.
- 2026-06-25T16:35:49.193338983+00:00 Task pending eval (agent reported done; awaiting `.evaluate-*` to score)
- 2026-06-25T16:46:28.871611846+00:00 FLIP failure was evaluator infrastructure, not analysis failure: inline FLIP Codex call timed out with exit 124 while reading prompt from stdin after a warning about one corrupt WG agent-cache YAML file. The task itself produced outputs, committed 07df829, pushed branch wg/agent-2749/fig5-2kb-direct-similarity-pilot, and is pending eval.
- 2026-06-25T16:47:17.440771081+00:00 PendingEval → Done (evaluator passed; downstream unblocks)