update-revise-phr-2

Metadata

Status	done
Assigned	`agent-427`
Agent identity	`f51439356729d112a6c404803d88015d5b44832c6c584c62b96732b63c2b0c7e`
Created	2026-04-01T19:18:24.676563352+00:00
Started	2026-04-02T01:22:38.278873690+00:00
Completed	2026-04-02T01:26:43.370210091+00:00
Tags	`edit,paper`, `eval-scheduled`
Tokens	455586 in / 7632 out
Eval score	0.96
└ hallucination rate	0.10
└ requirement coverage	0.95
└ semantic match	1.00
└ specificity match	0.95

Description

Goal

Update phr_gene_enrichment_synthesis.md to incorporate copy-aware findings as the central result.

Context

Read copy_aware_findings_summary.md (from review-extract-and task) for the data.

This synthesis doc was written before the copy-aware analysis. It needs to:

Center on copy-aware results as the key finding
Explain that standard ORA misses the multi-copy nature of PHR genes
Present the strengthened olfactory and immune signals with specific numbers
Include copy counts for each gene family
List ALL chromosome arms for each gene family (not just 1-2)

Validation

Copy-aware results are the central narrative
Numbers match the data files
Multi-arm gene locations are complete

## Goal
Update `phr_gene_enrichment_synthesis.md` to incorporate copy-aware findings as the central result.

## Context
Read `copy_aware_findings_summary.md` (from review-extract-and task) for the data.

This synthesis doc was written before the copy-aware analysis. It needs to:
- Center on copy-aware results as the key finding
- Explain that standard ORA misses the multi-copy nature of PHR genes
- Present the strengthened olfactory and immune signals with specific numbers
- Include copy counts for each gene family
- List ALL chromosome arms for each gene family (not just 1-2)

## Validation
- Copy-aware results are the central narrative
- Numbers match the data files
- Multi-arm gene locations are complete

Depends on

Required by

done validate-cross-check

Log

2026-04-01T19:18:24.669560629+00:00 Task paused
2026-04-01T19:19:07.978849069+00:00 Task published
2026-04-01T19:19:24.636870031+00:00 Lightweight assignment: agent=Careful Programmer (f5143935), exec_mode=full, context_scope=task, reason=Careful Programmer's precision-focused tradeoff matches the validation and accuracy requirements (matching numbers, completing multi-arm locations); document revision is methodical implementation work.
2026-04-01T19:22:50.220423357+00:00 Spawned by coordinator --executor claude --model claude-sonnet-4-20250514
2026-04-01T19:23:11.098517154+00:00 Starting task - will read copy_aware_findings_summary.md and current synthesis file
2026-04-01T19:23:30.291560924+00:00 Read both files. Need to completely reframe synthesis around copy-aware findings - olfactory now dominates (598x), transcription regulation emerges (928x), standard ORA missed true architecture
2026-04-01T19:24:42.124474133+00:00 Completed full rewrite of synthesis file - centered on copy-aware results with olfactory 598x, transcription 928x, GTP 309x enrichments. Included complete chromosome arms and copy counts.
2026-04-01T19:25:10.602527016+00:00 Validating work - checking copy-aware results are central (✅), verifying numbers match data, confirming multi-arm locations complete
2026-04-01T19:25:50.021152055+00:00 Validation issue found - chromosome arms need correction. OR4F17 is on chr1p,chr2p,chr3p,chr4p,chr5p,chr6p,chr7p,chr8p,chr9p,chrXp,chrYp,chr10p,chr11p,chr12p,chr15p,chr16p,chr17p,chr19p,chr20p,chr21p not what I listed
2026-04-01T19:26:00.447649528+00:00 Task marked as failed: Agent exited with code 1
2026-04-02T01:22:35.977220943+00:00 Task reset for retry (attempt #2)
2026-04-02T01:22:38.278875674+00:00 Spawned by coordinator --executor claude --model claude-sonnet-4-20250514
2026-04-02T01:22:58.973850878+00:00 Starting task review - checking existing work and files
2026-04-02T01:23:24.088907250+00:00 Examining existing synthesis file - previous agent completed comprehensive rewrite, checking for chromosome arm validation issues
2026-04-02T01:23:46.913716597+00:00 Found chromosome arm validation issues - OR4F17 data in file doesn't match CSV data. Missing chrX, chrY. Including incorrect chr13, chr14, chr18, chr22.
2026-04-02T01:24:03.238228661+00:00 Correcting chromosome arm data for all OR genes based on CSV file validation
2026-04-02T01:26:00.293428378+00:00 Completed chromosome arm corrections for all gene families: OR genes, immune genes, transcription genes, and GTP binding genes
2026-04-02T01:26:25.751974844+00:00 Validation complete: ✅ Copy-aware results are central narrative ✅ Numbers match data files ✅ Multi-arm gene locations are complete
2026-04-02T01:26:36.770057840+00:00 Committed: 4482242 — pushed to remote
2026-04-02T01:26:43.370212426+00:00 Task marked as done