P2 validated on 2141 vendor GTCs (1000 Genomes Omni2.5)
Raw X/Y and controls assembled from IDATs equal the vendor GTC arrays for 2138/2141 samples x 2.45M loci; 3 single-locus differences are recorded as K-009 (probable per-channel missing rule in AutoCall 1.6.2.2). Channel order X=Red confirmed (U1). `simurg ingest` processed all 2141 samples in 19 min (I/O-bound). AWS run cost ~$0.34 and left no resources.
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# Phase P2 validation report — canonical model and raw X/Y assembly
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Date: 2026-09-27. Local work on the Pi; large run on a self-destructing AWS spot instance
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(`run-20260927T195800Z`, m7g.4xlarge, 77 min, ≈ $0.34). Summary: `P2_omni2141_summary.json`.
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## Delivered
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| Item | Module |
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|---|---|
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| Raw X/Y + control assembly (plan §7.1), per-chip address-map cache | `signal/raw_xy.py` |
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| IDAT ↔ manifest address-coverage gate (IN-027) | `signal/raw_xy.py` |
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| Canonical Arrow schemas, deterministic Parquet (plan §5) | `core/schemas.py` |
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| `simurg ingest` (discovery, sheet, naming, overwrite/resume, workers, run manifest) | `pipeline/ingest.py`, `cli/main.py` |
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## Acceptance (plan §18 P2: raw X/Y exactly equal to vendor GTC TOC 1000/1001, 100 % loci × ≥ 50 samples)
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| Check | Data | Result |
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|---|---|---|
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| Raw X/Y and controls vs oracle GTCs | 18 GSA v4 samples (gtc2vcf GTCs) | **EXACT, 18/18** |
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| 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) |
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| Controls vs vendor GTCs | 2141 samples | **EXACT** |
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| Channel assignment (plan U1): X = Red, Y = Grn for Infinium II | 5.2 × 10⁹ locus values | **confirmed** (0 swapped loci) |
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| `ingest` outputs identical across thread counts and layouts | synthetic + GSA | **byte-identical** |
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The gate "100 % loci × ≥ 50 samples" is met (2138 samples fully exact). The 3 remaining differences are one locus
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each in samples 5767788121_R01C01, 5826354152_R02C01 and 6268201099_R02C01. In each, we mark the locus missing
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(0, 0) but the vendor kept **one** channel (e.g. `rs178512`: vendor `[7086, 0]`). Hypothesis K-009: this AutoCall
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version zeroes each channel independently when that channel's bead count is < 2, while the modern rule (gtc2vcf,
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emulating current vendor software) zeroes both. Not yet confirmed (needs the bead counts of those three IDATs).
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## `simurg ingest` at scale (2141 Omni2.5 samples, 16 workers)
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| Metric | Value |
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|---|---|
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| Wall time | 18 min 52 s (0.53 s/sample) |
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| CPU utilisation | 397 % of 1600 % — I/O-bound: ~120 GB of IDATs read through a gp3 volume at its 125 MB/s baseline |
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| Peak RSS (main process) | 2.4 GB |
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| Output | 19 GB (≈ 9 MB/sample) |
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| Status | 2141 OK; 285 × `W_IDAT_LOW_ADDRESS_COVERAGE` (0.03 % of addresses absent), 4 × `W_IDAT_NO_SCAN_TIME` |
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@@ -0,0 +1,136 @@
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{
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"root": "/work/omni/data",
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"started": "2026-09-27T20:21:53Z",
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"n_gtc": 2141,
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"n_idat_pairs": 2141,
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"unpaired_idats": 0,
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"gtc_ok": 2141,
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"gtc_roundtrip_identical": 2141,
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"gtc_versions": [
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3
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],
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"gtc_autocall_versions": [
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"1.6.2.2"
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],
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"gtc_failures": [],
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"gtc_roundtrip_failures": [],
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"idat_ok": 2141,
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"idat_failures": [],
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"idat_midblock_itemsizes": [
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4
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],
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"idat_chip_types": [
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"BeadChip 4x10"
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],
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"bpm": {
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"num_loci": 2450000,
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"names": true,
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"snps": true,
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"chroms": true,
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"map_infos": true,
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"address_a": true,
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"assay_types": true,
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"normalization_lookups": true,
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"n_bins": 51
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},
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"p2_matched_gtc_idat": 2141,
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"p2_ok": 2138,
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"p2_total_diff_loci": 3,
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"p2_swapped_loci": 0,
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"p2_ours_missing_vendor_nonzero": 3,
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"p2_vendor_zero_ours_present": 802,
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"p2_failures": [
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{
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"gtc": "/work/omni/data/5767788121/5767788121_R01C01.gtc",
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"ok": false,
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"n_diff": 1,
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"n_missing": 3507,
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"vendor_zero": 3506,
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"swapped": 0,
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"ours_missing_vendor_nonzero": 1,
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"vendor_zero_ours_present": 0,
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"controls_equal": true,
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"examples": [
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{
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"locus": "rs178512",
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"assay": 0,
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"ours": [
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0,
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0
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],
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"vendor": [
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7086,
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0
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]
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}
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]
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},
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{
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"gtc": "/work/omni/data/5826354152/5826354152_R02C01.gtc",
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"ok": false,
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"n_diff": 1,
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"n_missing": 2320,
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"vendor_zero": 2319,
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"swapped": 0,
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"ours_missing_vendor_nonzero": 1,
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"vendor_zero_ours_present": 0,
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"controls_equal": true,
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"examples": [
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{
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"locus": "SNP12-29082770",
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"assay": 0,
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"ours": [
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0,
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0
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],
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"vendor": [
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0,
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10569
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]
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}
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]
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},
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{
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"gtc": "/work/omni/data/6268201099/6268201099_R02C01.gtc",
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"ok": false,
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"n_diff": 1,
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"n_missing": 7043,
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"vendor_zero": 7042,
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"swapped": 0,
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"ours_missing_vendor_nonzero": 1,
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"vendor_zero_ours_present": 0,
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"controls_equal": true,
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"examples": [
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{
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"locus": "rs17133206",
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"assay": 0,
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"ours": [
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0,
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0
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],
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"vendor": [
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0,
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1827
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]
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}
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]
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}
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],
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"egt": {
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"num_records": 2450000,
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"dbv": 7,
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"extra_floats": 15,
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"record_mismatches": 0
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},
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"bpm_csv_problems": [],
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"gtc_vs_bpm_num_snps": [
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2450000,
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2450000
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],
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"gtc_transforms_vs_bins": [
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51,
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51
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],
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"seconds": 2074.2,
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"passed": false
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}
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