# Phase P2 validation report — canonical model and raw X/Y assembly

Date: 2026-09-27. Local work on the Pi; large run on a self-destructing AWS spot instance
(`run-20260927T195800Z`, m7g.4xlarge, 77 min, ≈ $0.34). Summary: `P2_omni2141_summary.json`.

## Delivered

| Item | Module |
|---|---|
| Raw X/Y + control assembly (plan §7.1), per-chip address-map cache | `signal/raw_xy.py` |
| IDAT ↔ manifest address-coverage gate (IN-027) | `signal/raw_xy.py` |
| Canonical Arrow schemas, deterministic Parquet (plan §5) | `core/schemas.py` |
| `simurg ingest` (discovery, sheet, naming, overwrite/resume, workers, run manifest) | `pipeline/ingest.py`, `cli/main.py` |

## Acceptance (plan §18 P2: raw X/Y exactly equal to vendor GTC TOC 1000/1001, 100 % loci × ≥ 50 samples)

| Check | Data | Result |
|---|---|---|
| Raw X/Y and controls vs oracle GTCs | 18 GSA v4 samples (gtc2vcf GTCs) | **EXACT, 18/18** |
| Raw X/Y vs **vendor** GTCs (AutoCall 1.6.2.2) | 2141 Omni2.5 samples × 2 450 000 loci | **2138/2141 samples EXACT**; 3 loci in 3 samples differ (below) |
| Controls vs vendor GTCs | 2141 samples | **EXACT** |
| Channel assignment (plan U1): X = Red, Y = Grn for Infinium II | 5.2 × 10⁹ locus values | **confirmed** (0 swapped loci) |
| `ingest` outputs identical across thread counts and layouts | synthetic + GSA | **byte-identical** |

The gate "100 % loci × ≥ 50 samples" is met (2138 samples fully exact). The 3 remaining differences are one locus
each in samples 5767788121_R01C01, 5826354152_R02C01 and 6268201099_R02C01. In each, we mark the locus missing
(0, 0) but the vendor kept **one** channel (e.g. `rs178512`: vendor `[7086, 0]`). Hypothesis K-009: this AutoCall
version zeroes each channel independently when that channel's bead count is < 2, while the modern rule (gtc2vcf,
emulating current vendor software) zeroes both. Not yet confirmed (needs the bead counts of those three IDATs).

## `simurg ingest` at scale (2141 Omni2.5 samples, 16 workers)

| Metric | Value |
|---|---|
| Wall time | 18 min 52 s (0.53 s/sample) |
| CPU utilisation | 397 % of 1600 % — I/O-bound: ~120 GB of IDATs read through a gp3 volume at its 125 MB/s baseline |
| Peak RSS (main process) | 2.4 GB |
| Output | 19 GB (≈ 9 MB/sample) |
| Status | 2141 OK; 285 × `W_IDAT_LOW_ADDRESS_COVERAGE` (0.03 % of addresses absent), 4 × `W_IDAT_NO_SCAN_TIME` |