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. Co-Authored-By: Claude Opus 5.5 <[email protected]> Claude-Session: https://claude.ai/code/session_01814GKVzZVL3FuF3DeiZXhv
2026-09-27 22:19:28 +01:00
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+{
+  "root": "/work/omni/data",
+  "started": "2026-09-27T20:21:53Z",
+  "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
+  },
+  "p2_matched_gtc_idat": 2141,
+  "p2_ok": 2138,
+  "p2_total_diff_loci": 3,
+  "p2_swapped_loci": 0,
+  "p2_ours_missing_vendor_nonzero": 3,
+  "p2_vendor_zero_ours_present": 802,
+  "p2_failures": [
+    {
+      "gtc": "/work/omni/data/5767788121/5767788121_R01C01.gtc",
+      "ok": false,
+      "n_diff": 1,
+      "n_missing": 3507,
+      "vendor_zero": 3506,
+      "swapped": 0,
+      "ours_missing_vendor_nonzero": 1,
+      "vendor_zero_ours_present": 0,
+      "controls_equal": true,
+      "examples": [
+        {
+          "locus": "rs178512",
+          "assay": 0,
+          "ours": [
+            0,
+            0
+          ],
+          "vendor": [
+            7086,
+            0
+          ]
+        }
+      ]
+    },
+    {
+      "gtc": "/work/omni/data/5826354152/5826354152_R02C01.gtc",
+      "ok": false,
+      "n_diff": 1,
+      "n_missing": 2320,
+      "vendor_zero": 2319,
+      "swapped": 0,
+      "ours_missing_vendor_nonzero": 1,
+      "vendor_zero_ours_present": 0,
+      "controls_equal": true,
+      "examples": [
+        {
+          "locus": "SNP12-29082770",
+          "assay": 0,
+          "ours": [
+            0,
+            0
+          ],
+          "vendor": [
+            0,
+            10569
+          ]
+        }
+      ]
+    },
+    {
+      "gtc": "/work/omni/data/6268201099/6268201099_R02C01.gtc",
+      "ok": false,
+      "n_diff": 1,
+      "n_missing": 7043,
+      "vendor_zero": 7042,
+      "swapped": 0,
+      "ours_missing_vendor_nonzero": 1,
+      "vendor_zero_ours_present": 0,
+      "controls_equal": true,
+      "examples": [
+        {
+          "locus": "rs17133206",
+          "assay": 0,
+          "ours": [
+            0,
+            0
+          ],
+          "vendor": [
+            0,
+            1827
+          ]
+        }
+      ]
+    }
+  ],
+  "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": 2074.2,
+  "passed": false
+}