P1 validated on 1000 Genomes Omni2.5 (2141 vendor GTCs + IDATs)

All 2141 vendor-written GTC v3 files match BeadArrayFiles field by field and re-encode byte-identically; all IDAT pairs parse; the 2.45M-locus BPM, dbv-7 EGT and CSV manifest agree with BeadArrayFiles and each other. Run on a self-destructing AWS spot instance (42 min, ~$0.20). Co-Authored-By: Claude Opus 5.5 <[email protected]> Claude-Session: https://claude.ai/code/session_01814GKVzZVL3FuF3DeiZXhv
2026-09-27 20:22:35 +01:00
1 parent f52313fc93
commit 854fe132cc
@@ -37,6 +37,22 @@ Commands: `pytest tests/unit` (every CI run), `pytest tests/oracle -m "not slow"
 | Sample-sheet matrix EDGE-007 (27 cases) incl. 10 000 rows < 2 s (PERF-007) | synthetic | **pass** |
 | Locale independence of `inspect --json` (C, tr_TR, de_DE) | synthetic | **pass** |

+## Large-scale run: 1000 Genomes Omni2.5 (AWS, 2026-09-27)
+
+Self-destructing spot instance (`scripts/cloud/trial.sh`, m7g.4xlarge, 16 vCPU), run `run-20260927T183712Z`,
+summary in `P1_omni2141_summary.json`. 107 GB archive streamed from `s3://1000genomes` (extracted 170 GB) in
+22 min; validation 18 min; instance lifetime 42 min; cost ≈ $0.20.
+
+| Criterion | Result |
+|---|---|
+| 2141 **vendor-written** GTCs (v3, AutoCall 1.6.2.2): every field equal to BeadArrayFiles | **2141/2141 EXACT** |
+| Same GTCs: read → write byte-identical | **2141/2141** |
+| 2141 IDAT pairs (BeadChip 4x10) parse and pair; MidBlock int32 | **2141/2141** |
+| BPM HumanOmni2.5-4v1-Multi_B (2 450 000 loci, 51 normalization bins) vs BeadArrayFiles | **EXACT** |
+| EGT (data block v7, 2 450 000 records) vs BeadArrayFiles: all θ/R means and SDs, N | **0 mismatches** |
+| BPM ↔ CSV consistency | **0 differences** |
+| GTC transforms per sample = BPM bins (51) | **pass** |
+
 ## Performance on the Pi (single thread, pure Python/NumPy)

 | Operation | Time | Peak RSS |
@@ -51,8 +67,5 @@ BPM/CSV parsing is the only slow step; it is a one-off per run and moves to Rust

 ## Not yet covered (needs the larger machine / later phases)

- GEO sweep of 254 genotyping IDAT series and the 1000 Genomes Omni2.5 set (plan §18 P1 wording) — P1 is
-  validated on P0 data only; rerun `tests/oracle` after `scripts/fetch_data.sh p1`.
- GTCs written by vendor software (only gtc2vcf-written GTCs are available locally); the 1000 Genomes Broad set
-  contains vendor GTCs.
+- GEO sweep of 254 genotyping IDAT series (other chip generations, IDAT variants) — still open.
 - IN-027 (IDAT ↔ manifest coverage gate) is P2; the coverage computation is already exercised by a test.
@@ -0,0 +1,53 @@
+{
+  "root": "/work/omni/data",
+  "started": "2026-09-27T19:00:42Z",
+  "n_gtc": 2141,
+  "n_idat_pairs": 2141,
+  "unpaired_idats": 0,
+  "gtc_ok": 2141,
+  "gtc_roundtrip_identical": 2141,
+  "gtc_versions": [
+    3
+  ],
+  "gtc_autocall_versions": [
+    "1.6.2.2"
+  ],
+  "gtc_failures": [],
+  "gtc_roundtrip_failures": [],
+  "idat_ok": 2141,
+  "idat_failures": [],
+  "idat_midblock_itemsizes": [
+    4
+  ],
+  "idat_chip_types": [
+    "BeadChip 4x10"
+  ],
+  "bpm": {
+    "num_loci": 2450000,
+    "names": true,
+    "snps": true,
+    "chroms": true,
+    "map_infos": true,
+    "address_a": true,
+    "assay_types": true,
+    "normalization_lookups": true,
+    "n_bins": 51
+  },
+  "egt": {
+    "num_records": 2450000,
+    "dbv": 7,
+    "extra_floats": 15,
+    "record_mismatches": 0
+  },
+  "bpm_csv_problems": [],
+  "gtc_vs_bpm_num_snps": [
+    2450000,
+    2450000
+  ],
+  "gtc_transforms_vs_bins": [
+    51,
+    51
+  ],
+  "seconds": 1098.7,
+  "passed": true
+}