survey-pipeline-section

Metadata

Status	done
Assigned	`agent-635`
Agent identity	`3184716484e6f0ea08bb13539daf07686ee79d440505f1fdf2de0357707034c3`
Created	2026-05-04T22:32:46.190143401+00:00
Started	2026-05-04T22:44:43.875415030+00:00
Completed	2026-05-04T23:06:47.306778967+00:00
Tags	`paper-prep,survey`, `eval-scheduled`
Tokens	1875079 in / 4370 out
Eval score	0.75
└ blocking impact	0.75
└ completeness	0.78
└ coordination overhead	0.75
└ correctness	0.70
└ downstream usability	0.78
└ efficiency	0.85
└ intent fidelity	0.54
└ style adherence	0.85

Description

Key findings (numbered list, with concrete metrics — counts, percentages, p-values, effect sizes)
Existing figures/plots referenced (with paths if present in the file)
Existing data tables/CSVs referenced (paths)
Statistical/computational methods used
Open gaps — analyses or figures that would need to be (re)generated for a Nature-style manuscript
Suggested figures (main + extended/SI) with one-line caption ideas (mark whether each is already produced or needs generation)
Suggested talk slides with one-line takeaway each OUTPUT: paper_prep/surveys/SURVEY_01_pipeline.md following the 7-section structure above. ACCEPTANCE: File exists, contains all 7 numbered sections, mentions concrete figure paths or data files where present, <= 800 lines.

INPUT: end-to-end-report/report/01_pipeline.md (read fully).
CONTEXT: We are preparing a Nature manuscript + 15-min talk on subtelomeric sequence sharing across HPRCv2 (233 samples, 465 haplotypes, 15 arm-level + 50 sequence-level communities) validated by 3D genome data. This task surveys ONE section of the existing end-to-end report.
TASK: Extract from the input file:
1. Key findings (numbered list, with concrete metrics — counts, percentages, p-values, effect sizes)
2. Existing figures/plots referenced (with paths if present in the file)
3. Existing data tables/CSVs referenced (paths)
4. Statistical/computational methods used
5. Open gaps — analyses or figures that would need to be (re)generated for a Nature-style manuscript
6. Suggested figures (main + extended/SI) with one-line caption ideas (mark whether each is already produced or needs generation)
7. Suggested talk slides with one-line takeaway each
OUTPUT: paper_prep/surveys/SURVEY_01_pipeline.md following the 7-section structure above.
ACCEPTANCE: File exists, contains all 7 numbered sections, mentions concrete figure paths or data files where present, <= 800 lines.

Depends on

done .assign-survey-pipeline-section

Required by

Log

2026-05-04T22:32:46.176663510+00:00 Task paused
2026-05-04T22:33:33.760195919+00:00 Task published
2026-05-04T22:44:43.875418647+00:00 Spawned by coordinator --executor claude --model opus
2026-05-04T22:45:21.280956600+00:00 Starting: reading 01_pipeline.md and preparing survey output. Note: role says Evaluator but task description is actor work (produce survey file). Proceeding with actor work since acceptance criteria specify file production.
2026-05-04T22:50:08.950303408+00:00 Wrote SURVEY_01_pipeline.md (157 lines, all 7 numbered sections, concrete data paths from source). Validated against acceptance: file exists, 7 sections, paths cited, <= 800 lines.
2026-05-04T22:50:51.164134139+00:00 Committed: 3862eb5 — pushed to origin/wg/agent-635/survey-pipeline-section
2026-05-04T23:06:47.306781622+00:00 Task pending eval (agent reported done; awaiting `.evaluate-*` to score)
2026-05-04T23:10:53.940577072+00:00 PendingEval → Done (evaluator passed; downstream unblocks)