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map_variants/Africa_1T12/v1_true/estimates/audit-compare-51974588.json

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map_variants/Africa_1T12/v1_true/estimates/compare_source_final_51974588.json

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map_variants/Africa_1T12/v1_true/estimates/final/SCORE_MANIFEST.json

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+    "present_sha256": "b2d9e652535fb0ca5d60ca9d8b595249dc1cf8d4cb36025a54a50e4458048ef8"
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+}

map_variants/Africa_1T12/v1_true/estimates/t0_final_51974588.json

@@ -0,0 +1,102 @@
+{
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+    "same_members": {
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+}

map_variants/Africa_1T12/v1_true/necast_inputs/COHORT_RECEIPT.json

@@ -0,0 +1,45 @@
+{
+ "cohort": "/ibex/project/c2041/hany0c/bench_h2h_20260915/cohort/mapvar/v2_b_Africa_1T12__v1_true",
+ "dataset_root": "/ibex/project/c2041/hany0c/bench_h2h_20260915/mapvar/data/v2_b_Africa_1T12__v1_true",
+ "dataset_root_files": {
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+ },
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+ "job": "51966345_0",
+ "level32_rows": 11,
+ "schema": "bench_h2h.map_variants.cohort_receipt/1",
+ "source_cohort": "/ibex/project/c2041/hany0c/bench_h2h_20260915/cohort/v2_b_Africa_1T12",
+ "variant": "v1_true"
+}

map_variants/Africa_1T12/v1_true/necast_inputs/freeze/architecture_split.jsonl

@@ -0,0 +1,12 @@
+{"architecture_group": "bench:fcfc6558a872139a7f4afc58dac2401b41847cad39c775c64bc96f85cacb471b:00000000", "canonical_id": "fcfc6558a872139a7f4afc58dac2401b41847cad39c775c64bc96f85cacb471b:00000000", "seed": 2072748958, "split": "validation"}
+{"architecture_group": "bench:fcfc6558a872139a7f4afc58dac2401b41847cad39c775c64bc96f85cacb471b:00000001", "canonical_id": "fcfc6558a872139a7f4afc58dac2401b41847cad39c775c64bc96f85cacb471b:00000001", "seed": 2072756877, "split": "validation"}
+{"architecture_group": "bench:fcfc6558a872139a7f4afc58dac2401b41847cad39c775c64bc96f85cacb471b:00000002", "canonical_id": "fcfc6558a872139a7f4afc58dac2401b41847cad39c775c64bc96f85cacb471b:00000002", "seed": 2072764796, "split": "validation"}
+{"architecture_group": "bench:fcfc6558a872139a7f4afc58dac2401b41847cad39c775c64bc96f85cacb471b:00000003", "canonical_id": "fcfc6558a872139a7f4afc58dac2401b41847cad39c775c64bc96f85cacb471b:00000003", "seed": 2072772715, "split": "validation"}
+{"architecture_group": "bench:fcfc6558a872139a7f4afc58dac2401b41847cad39c775c64bc96f85cacb471b:00000004", "canonical_id": "fcfc6558a872139a7f4afc58dac2401b41847cad39c775c64bc96f85cacb471b:00000004", "seed": 2072780634, "split": "validation"}
+{"architecture_group": "bench:fcfc6558a872139a7f4afc58dac2401b41847cad39c775c64bc96f85cacb471b:00000005", "canonical_id": "fcfc6558a872139a7f4afc58dac2401b41847cad39c775c64bc96f85cacb471b:00000005", "seed": 2072788553, "split": "validation"}
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map_variants/Africa_1T12/v1_true/necast_inputs/freeze/open_audit.json

@@ -0,0 +1,94 @@
+{
+ "opened": [
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+  },
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+  },
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+  },
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+  },
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+  },
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+  },
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+  },
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+  },
+  {
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+  },
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+  },
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+  },
+  {
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+  },
+  {
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+  },
+  {
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+   "path": "/ibex/project/c2041/hany0c/bench_h2h_20260915/cohort/mapvar/v2_b_Africa_1T12__v1_true/freeze/sample_identities.jsonl"
+  },
+  {
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+  },
+  {
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+   "path": "/ibex/project/c2041/hany0c/bench_h2h_20260915/cohort/mapvar/v2_b_Africa_1T12__v1_true/freeze/reference_cache.npz"
+  },
+  {
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+   "path": "/ibex/project/c2041/hany0c/bench_h2h_20260915/cohort/mapvar/v2_b_Africa_1T12__v1_true/freeze/sample_identities.jsonl"
+  },
+  {
+   "mode": "r",
+   "path": "/ibex/project/c2041/hany0c/bench_h2h_20260915/cohort/mapvar/v2_b_Africa_1T12__v1_true/freeze/architecture_split.jsonl"
+  },
+  {
+   "mode": "w",
+   "path": "/ibex/project/c2041/hany0c/bench_h2h_20260915/cohort/mapvar/v2_b_Africa_1T12__v1_true/freeze/report.json"
+  }
+ ],
+ "purposes": [
+  "bench",
+  "deploy",
+  "production_summary"
+ ],
+ "refused": []
+}

map_variants/Africa_1T12/v1_true/necast_inputs/freeze/report.json

@@ -0,0 +1,175 @@
+{
+  "benchmark_canonical_ids": [
+    "fcfc6558a872139a7f4afc58dac2401b41847cad39c775c64bc96f85cacb471b:00000000",
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+  "decoy_canonical_ids": [
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+    "fcfc6558a872139a7f4afc58dac2401b41847cad39c775c64bc96f85cacb471b:00000011"
+  ],
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+    "manifest_sha256": "659f0427dc079a0bdb2ad3ae8ff8a328e98df6eeeb623532c34cb9a2bcd0b502",
+    "path": "/ibex/project/c2041/hany0c/deploy_20260913_fixed32",
+    "verified_artifact_count": 34
+  },
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map_variants/Africa_1T12/v1_true/necast_inputs/freeze/sample_identities.jsonl

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map_variants/Africa_1T12/v1_true/necast_inputs/freeze/snapshot.json

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map_variants/Africa_1T12/v1_true/necast_inputs/level32/DONE.json

@@ -0,0 +1,29 @@
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+  "cache": "unphased_evidence_cache.npz",
+  "cache_contract": "dlcoalsim-unphased-evidence-v1",
+  "cache_sha256": "a3b0a2db12f8f8d7bd2102d0efd759d1fe80747bb14c5e067d9872d41e6b0f44",
+  "identities": "sample_identities.jsonl",
+  "identities_sha256": "7120ac8d73613869a73bc7cce26ecb48de29341afea438c858fd85ae560457e6",
+  "ladder_chain": 0,
+  "ladder_level": 32,
+  "report": "report.json",
+  "report_sha256": "6523c325334327645a40be4c8e00f7dd5fa6f9e86fb58824ad2d88940ae7186c",
+  "row_order_sha256": "8158795ec7a061fc5ac0526c168541121833e656e35ed2b9cb93c2035f999241",
+  "sample_metadata": "sample_metadata.jsonl",
+  "sample_metadata_sha256": "ace3342063e24b382707ac28e5d12bcd87d36e1e03dfb7ca0f52cecc4ac3c9e2",
+  "schema": "dlcoalsim-unphased-evidence-v1",
+  "schema_version": 1,
+  "selected_indices": "selected_indices.npy",
+  "selected_indices_sha256": "03cd6480c6fefdf8ecb1317d77b096c58a6cfd95a8177662c77b5cfd8c5f8380",
+  "snapshot": "snapshot.json",
+  "snapshot_sha256": "0d3fd70d6751861ce9af11de6f34578de363255d061c8230b849e0346f1de207",
+  "status": "complete",
+  "stream_presence_counts": {
+    "ibs": 11,
+    "ld": 11,
+    "nw": 11,
+    "sfs": 11
+  }
+}

map_variants/Africa_1T12/v1_true/necast_inputs/level32/PLAN.json

@@ -0,0 +1,230 @@
+{
+  "architecture_split_counts": {
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+    "1": 8,
+    "2": 0
+  },
+  "builder_deployment": null,
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+  "cache_contract_version": 1,
+  "command": [
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+    "--chain",
+    "0",
+    "--level",
+    "32",
+    "--snapshot",
+    "/ibex/project/c2041/hany0c/bench_h2h_20260915/cohort/mapvar/v2_b_Africa_1T12__v1_true/freeze/snapshot.json",
+    "--reference-cache",
+    "/ibex/project/c2041/hany0c/bench_h2h_20260915/cohort/mapvar/v2_b_Africa_1T12__v1_true/freeze/reference_cache.npz",
+    "--identities",
+    "/ibex/project/c2041/hany0c/bench_h2h_20260915/cohort/mapvar/v2_b_Africa_1T12__v1_true/freeze/sample_identities.jsonl",
+    "--architecture-split",
+    "/ibex/project/c2041/hany0c/bench_h2h_20260915/cohort/mapvar/v2_b_Africa_1T12__v1_true/freeze/architecture_split.jsonl",
+    "--out-dir",
+    "/ibex/project/c2041/hany0c/bench_h2h_20260915/cohort/mapvar/v2_b_Africa_1T12__v1_true/chain0_level32",
+    "--gate-samples",
+    "11",
+    "--workers",
+    "4",
+    "--source-root-map",
+    "/ibex/project/c2041/hany0c/bench_h2h_20260915/mapvar/data/v2_b_Africa_1T12__v1_true=/ibex/project/c2041/hany0c/bench_h2h_20260915/mapvar/data/.mirrors/v2_b_Africa_1T12__v1_true"
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+      8,
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+      "ibs0_gap_sequence_censored",
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+      "ibs0_contiguous_run",
+      "ibs1_contiguous_run",
+      "ibs2_contiguous_run"
+    ],
+    "ibs_schema": "diploid-ibs012-missing-cut-log2bp-dyadic-v1",
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+    "callable_leaf_policy": "recomputed from the level's own states; never a C(L,2)/C(32,2) rescale of the top level, which disagrees with the level's own spectrum whenever calls are missing",
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+    "sfs_projected_n": 32,
+    "stream_names": [
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+    "window_pyramid_policy": "features/context are normalised by 2L, the rung's own haplotype count, not by the padded packed width: the padded slots decode as homozygous reference and contribute nothing to an allele count, so dividing by them would shrink every window statistic at levels 1 and 2 and would state the wrong sample size in the context channel"
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+    "/ibex/project/c2041/hany0c/bench_h2h_20260915/mapvar/data/v2_b_Africa_1T12__v1_true": "/ibex/project/c2041/hany0c/bench_h2h_20260915/mapvar/data/.mirrors/v2_b_Africa_1T12__v1_true"
+  },
+  "reference_architecture_split": "/ibex/project/c2041/hany0c/bench_h2h_20260915/cohort/mapvar/v2_b_Africa_1T12__v1_true/freeze/architecture_split.jsonl",
+  "reference_architecture_split_sha256": "7fc3c7f026176332e7a7b92f7a1a9c8bcfc168e76fbac8015dcdbb9f1166bf9c",
+  "reference_cache": "/ibex/project/c2041/hany0c/bench_h2h_20260915/cohort/mapvar/v2_b_Africa_1T12__v1_true/freeze/reference_cache.npz",
+  "reference_cache_access_policy": "sha256_only_never_numpy_loaded",
+  "reference_cache_sha256": "3d7f402c29bd32b8907ed13d78daabc08b4938de1a3b641e16567f8237ef98de",
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+  "row_selection": "none: every eligible development row is present",
+  "schema": "dlcoalsim-unphased-evidence-v1",
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+  "selected_samples": 11,
+  "selection_seal": "architecture code 2 is removed before row-specific variant, raw, target, or metadata task construction",
+  "snapshot": "/ibex/project/c2041/hany0c/bench_h2h_20260915/cohort/mapvar/v2_b_Africa_1T12__v1_true/freeze/snapshot.json",
+  "snapshot_sha256": "0d3fd70d6751861ce9af11de6f34578de363255d061c8230b849e0346f1de207",
+  "source_identities": "/ibex/project/c2041/hany0c/bench_h2h_20260915/cohort/mapvar/v2_b_Africa_1T12__v1_true/freeze/sample_identities.jsonl",
+  "source_identities_sha256": "c08dda7852209ba9f127b262710b227d9096aae4b911cff938ea8bbde2462f0c",
+  "source_samples": 12,
+  "status": "extracting",
+  "verify_source_sha256": true,
+  "workers": 4
+}

map_variants/Africa_1T12/v1_true/necast_inputs/level32/architecture_split.jsonl

@@ -0,0 +1,11 @@
+{"architecture_group": "bench:fcfc6558a872139a7f4afc58dac2401b41847cad39c775c64bc96f85cacb471b:00000000", "canonical_id": "fcfc6558a872139a7f4afc58dac2401b41847cad39c775c64bc96f85cacb471b:00000000", "seed": 2072748958, "split": "validation"}
+{"architecture_group": "bench:fcfc6558a872139a7f4afc58dac2401b41847cad39c775c64bc96f85cacb471b:00000001", "canonical_id": "fcfc6558a872139a7f4afc58dac2401b41847cad39c775c64bc96f85cacb471b:00000001", "seed": 2072756877, "split": "validation"}
+{"architecture_group": "bench:fcfc6558a872139a7f4afc58dac2401b41847cad39c775c64bc96f85cacb471b:00000002", "canonical_id": "fcfc6558a872139a7f4afc58dac2401b41847cad39c775c64bc96f85cacb471b:00000002", "seed": 2072764796, "split": "validation"}
+{"architecture_group": "bench:fcfc6558a872139a7f4afc58dac2401b41847cad39c775c64bc96f85cacb471b:00000003", "canonical_id": "fcfc6558a872139a7f4afc58dac2401b41847cad39c775c64bc96f85cacb471b:00000003", "seed": 2072772715, "split": "validation"}
+{"architecture_group": "bench:fcfc6558a872139a7f4afc58dac2401b41847cad39c775c64bc96f85cacb471b:00000004", "canonical_id": "fcfc6558a872139a7f4afc58dac2401b41847cad39c775c64bc96f85cacb471b:00000004", "seed": 2072780634, "split": "validation"}
+{"architecture_group": "bench:fcfc6558a872139a7f4afc58dac2401b41847cad39c775c64bc96f85cacb471b:00000005", "canonical_id": "fcfc6558a872139a7f4afc58dac2401b41847cad39c775c64bc96f85cacb471b:00000005", "seed": 2072788553, "split": "validation"}
+{"architecture_group": "bench:fcfc6558a872139a7f4afc58dac2401b41847cad39c775c64bc96f85cacb471b:00000006", "canonical_id": "fcfc6558a872139a7f4afc58dac2401b41847cad39c775c64bc96f85cacb471b:00000006", "seed": 2072796472, "split": "validation"}
+{"architecture_group": "bench:fcfc6558a872139a7f4afc58dac2401b41847cad39c775c64bc96f85cacb471b:00000007", "canonical_id": "fcfc6558a872139a7f4afc58dac2401b41847cad39c775c64bc96f85cacb471b:00000007", "seed": 2072804391, "split": "validation"}
+{"architecture_group": "bench:fcfc6558a872139a7f4afc58dac2401b41847cad39c775c64bc96f85cacb471b:00000008", "canonical_id": "fcfc6558a872139a7f4afc58dac2401b41847cad39c775c64bc96f85cacb471b:00000008", "seed": 2072812310, "split": "train"}
+{"architecture_group": "bench:fcfc6558a872139a7f4afc58dac2401b41847cad39c775c64bc96f85cacb471b:00000009", "canonical_id": "fcfc6558a872139a7f4afc58dac2401b41847cad39c775c64bc96f85cacb471b:00000009", "seed": 2072820229, "split": "train"}
+{"architecture_group": "bench:fcfc6558a872139a7f4afc58dac2401b41847cad39c775c64bc96f85cacb471b:00000010", "canonical_id": "fcfc6558a872139a7f4afc58dac2401b41847cad39c775c64bc96f85cacb471b:00000010", "seed": 2072828148, "split": "train"}

map_variants/Africa_1T12/v1_true/necast_inputs/level32/gate.json

@@ -0,0 +1,38 @@
+{
+  "eligible_development_samples": 11,
+  "logical_root_counts": {
+    "/ibex/project/c2041/hany0c/bench_h2h_20260915/mapvar/data/v2_b_Africa_1T12__v1_true": 11
+  },
+  "requested_samples": 11,
+  "schema": "dlcoal-ibs-tract-extreme-balanced-gate-v1",
+  "sealed_selection_samples_excluded_before_ranking": 1,
+  "selected_rows": [
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+    2,
+    3,
+    4,
+    5,
+    6,
+    7,
+    8,
+    9,
+    10
+  ],
+  "selected_variant_counts": [
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+    55873,
+    57157,
+    69161,
+    60241,
+    61594,
+    71263,
+    56515,
+    61129,
+    67362,
+    60817
+  ],
+  "selection": "balance logical dataset_root; alternate smallest/largest exact variant count; canonical_id tie break; publish reference row order",
+  "variant_count_max": 71263,
+  "variant_count_min": 55873
+}

map_variants/Africa_1T12/v1_true/necast_inputs/level32/report.json

@@ -0,0 +1,394 @@
+{
+  "architecture_split_counts": {
+    "0": 3,
+    "1": 8,
+    "2": 0
+  },
+  "array_shapes": {
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+      7,
+      31,
+      27
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+    "ladder_columns": [
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+      32
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+    "ladder_level": [
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+    "ld_bin_edges_morgan": [
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+    "ld_effective_individual_sums": [
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+      26
+    ],
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+    ],
+    "ld_lags": [
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+    "ld_pair_counts": [
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+    ],
+    "missing_call_counts": [
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+    "nw_log10": [
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+    ],
+    "nw_proxy": [
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+    ],
+    "packed_decoded_columns": [
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+    "packed_padded_columns": [
+      1
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+    "pair_coalescences_outside": [
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+    ],
+    "pair_coalescences_per_bin": [
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+      64
+    ],
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+    ],
+    "sequence_length_bp": [
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+    "sfs_bins_used": [
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+    "sfs_projected_n": [
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+    "sfs_retained_site_fraction": [
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+    "split": [
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+    "stream_names": [
+      4
+    ],
+    "stream_presence": [
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+      4
+    ],
+    "targets": [
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+      64
+    ],
+    "variant_counts": [
+      11
+    ]
+  },
+  "builder_deployment": null,
+  "cache": "/ibex/project/c2041/hany0c/bench_h2h_20260915/cohort/mapvar/v2_b_Africa_1T12__v1_true/chain0_level32/unphased_evidence_cache.npz",
+  "cache_contract": "dlcoalsim-unphased-evidence-v1",
+  "cache_contract_version": 1,
+  "cache_sha256": "a3b0a2db12f8f8d7bd2102d0efd759d1fe80747bb14c5e067d9872d41e6b0f44",
+  "cache_size_bytes": 1292608,
+  "command": [
+    "/ibex/project/c2041/hany0c/deploy_20260913_fixed32/scripts/build_level_cache.py",
+    "--chain",
+    "0",
+    "--level",
+    "32",
+    "--snapshot",
+    "/ibex/project/c2041/hany0c/bench_h2h_20260915/cohort/mapvar/v2_b_Africa_1T12__v1_true/freeze/snapshot.json",
+    "--reference-cache",
+    "/ibex/project/c2041/hany0c/bench_h2h_20260915/cohort/mapvar/v2_b_Africa_1T12__v1_true/freeze/reference_cache.npz",
+    "--identities",
+    "/ibex/project/c2041/hany0c/bench_h2h_20260915/cohort/mapvar/v2_b_Africa_1T12__v1_true/freeze/sample_identities.jsonl",
+    "--architecture-split",
+    "/ibex/project/c2041/hany0c/bench_h2h_20260915/cohort/mapvar/v2_b_Africa_1T12__v1_true/freeze/architecture_split.jsonl",
+    "--out-dir",
+    "/ibex/project/c2041/hany0c/bench_h2h_20260915/cohort/mapvar/v2_b_Africa_1T12__v1_true/chain0_level32",
+    "--gate-samples",
+    "11",
+    "--workers",
+    "4",
+    "--source-root-map",
+    "/ibex/project/c2041/hany0c/bench_h2h_20260915/mapvar/data/v2_b_Africa_1T12__v1_true=/ibex/project/c2041/hany0c/bench_h2h_20260915/mapvar/data/.mirrors/v2_b_Africa_1T12__v1_true"
+  ],
+  "development_eligible_samples": 11,
+  "extraction_seconds": 4.71747257001698,
+  "feature_semantics": {
+    "diploid_state_schema": "diploid-six-state-adjacent-haplotypes-v1",
+    "folded_sfs": "missing-aware hypergeometric projection to n=32 then 16-bin fold",
+    "genotype_ld_schema": "registered-site-lag-genotype-dose-r2-v1",
+    "genotype_ld_site_lags": [
+      1,
+      2,
+      4,
+      8,
+      16,
+      32,
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+      "ibs0_contiguous_run",
+      "ibs1_contiguous_run",
+      "ibs2_contiguous_run"
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+    "output": "direct 64-bin residual target only"
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+    "log1p_eligible_site_pair_count"
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+  },
+  "reference_architecture_split": "/ibex/project/c2041/hany0c/bench_h2h_20260915/cohort/mapvar/v2_b_Africa_1T12__v1_true/freeze/architecture_split.jsonl",
+  "reference_architecture_split_sha256": "7fc3c7f026176332e7a7b92f7a1a9c8bcfc168e76fbac8015dcdbb9f1166bf9c",
+  "reference_array_sha256": {
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+  "reference_cache": "/ibex/project/c2041/hany0c/bench_h2h_20260915/cohort/mapvar/v2_b_Africa_1T12__v1_true/freeze/reference_cache.npz",
+  "reference_cache_access_policy": "sha256_only_never_numpy_loaded",
+  "reference_cache_sha256": "3d7f402c29bd32b8907ed13d78daabc08b4938de1a3b641e16567f8237ef98de",
+  "region_counts": [
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+  "row_selection": "none: every eligible development row is present",
+  "sample_metadata_sha256": "ace3342063e24b382707ac28e5d12bcd87d36e1e03dfb7ca0f52cecc4ac3c9e2",
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+  "selected_samples": 11,
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+  "sfs_retained_site_fraction_mean": 1.0,
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+  "snapshot": "/ibex/project/c2041/hany0c/bench_h2h_20260915/cohort/mapvar/v2_b_Africa_1T12__v1_true/freeze/snapshot.json",
+  "snapshot_sha256": "0d3fd70d6751861ce9af11de6f34578de363255d061c8230b849e0346f1de207",
+  "source_identities": "/ibex/project/c2041/hany0c/bench_h2h_20260915/cohort/mapvar/v2_b_Africa_1T12__v1_true/freeze/sample_identities.jsonl",
+  "source_identities_sha256": "c08dda7852209ba9f127b262710b227d9096aae4b911cff938ea8bbde2462f0c",
+  "source_samples": 12,
+  "status": "complete",
+  "stream_presence_counts": {
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+    "ld": 11,
+    "nw": 11,
+    "sfs": 11
+  },
+  "total_ld_eligible_pairs": 3841808,
+  "total_variants": 679489,
+  "verify_source_sha256": true,
+  "workers": 4
+}

map_variants/Africa_1T12/v1_true/necast_inputs/level32/sample_identities.jsonl

@@ -0,0 +1,11 @@
+{"canonical_id": "fcfc6558a872139a7f4afc58dac2401b41847cad39c775c64bc96f85cacb471b:00000000", "dataset_root": "/ibex/project/c2041/hany0c/bench_h2h_20260915/mapvar/data/v2_b_Africa_1T12__v1_true", "demography_type": "stdpopsim", "literature_model_id": "BENCH_Africa_1T12", "map_mode": "empirical_slice", "plan_sha256": "fcfc6558a872139a7f4afc58dac2401b41847cad39c775c64bc96f85cacb471b", "sample_id": "sim_00000000", "sample_index": 0, "scenario_key": "stdpopsim|empirical_slice|mild_noise", "seed": 2072748958, "slice_chrom": "chr13", "split": "validation"}
+{"canonical_id": "fcfc6558a872139a7f4afc58dac2401b41847cad39c775c64bc96f85cacb471b:00000001", "dataset_root": "/ibex/project/c2041/hany0c/bench_h2h_20260915/mapvar/data/v2_b_Africa_1T12__v1_true", "demography_type": "stdpopsim", "literature_model_id": "BENCH_Africa_1T12", "map_mode": "empirical_slice", "plan_sha256": "fcfc6558a872139a7f4afc58dac2401b41847cad39c775c64bc96f85cacb471b", "sample_id": "sim_00000001", "sample_index": 1, "scenario_key": "stdpopsim|empirical_slice|mild_noise", "seed": 2072756877, "slice_chrom": "chr4", "split": "validation"}
+{"canonical_id": "fcfc6558a872139a7f4afc58dac2401b41847cad39c775c64bc96f85cacb471b:00000002", "dataset_root": "/ibex/project/c2041/hany0c/bench_h2h_20260915/mapvar/data/v2_b_Africa_1T12__v1_true", "demography_type": "stdpopsim", "literature_model_id": "BENCH_Africa_1T12", "map_mode": "empirical_slice", "plan_sha256": "fcfc6558a872139a7f4afc58dac2401b41847cad39c775c64bc96f85cacb471b", "sample_id": "sim_00000002", "sample_index": 2, "scenario_key": "stdpopsim|empirical_slice|mild_noise", "seed": 2072764796, "slice_chrom": "chr13", "split": "validation"}
+{"canonical_id": "fcfc6558a872139a7f4afc58dac2401b41847cad39c775c64bc96f85cacb471b:00000003", "dataset_root": "/ibex/project/c2041/hany0c/bench_h2h_20260915/mapvar/data/v2_b_Africa_1T12__v1_true", "demography_type": "stdpopsim", "literature_model_id": "BENCH_Africa_1T12", "map_mode": "empirical_slice", "plan_sha256": "fcfc6558a872139a7f4afc58dac2401b41847cad39c775c64bc96f85cacb471b", "sample_id": "sim_00000003", "sample_index": 3, "scenario_key": "stdpopsim|empirical_slice|mild_noise", "seed": 2072772715, "slice_chrom": "chr13", "split": "validation"}
+{"canonical_id": "fcfc6558a872139a7f4afc58dac2401b41847cad39c775c64bc96f85cacb471b:00000004", "dataset_root": "/ibex/project/c2041/hany0c/bench_h2h_20260915/mapvar/data/v2_b_Africa_1T12__v1_true", "demography_type": "stdpopsim", "literature_model_id": "BENCH_Africa_1T12", "map_mode": "empirical_slice", "plan_sha256": "fcfc6558a872139a7f4afc58dac2401b41847cad39c775c64bc96f85cacb471b", "sample_id": "sim_00000004", "sample_index": 4, "scenario_key": "stdpopsim|empirical_slice|mild_noise", "seed": 2072780634, "slice_chrom": "chr2", "split": "validation"}
+{"canonical_id": "fcfc6558a872139a7f4afc58dac2401b41847cad39c775c64bc96f85cacb471b:00000005", "dataset_root": "/ibex/project/c2041/hany0c/bench_h2h_20260915/mapvar/data/v2_b_Africa_1T12__v1_true", "demography_type": "stdpopsim", "literature_model_id": "BENCH_Africa_1T12", "map_mode": "empirical_slice", "plan_sha256": "fcfc6558a872139a7f4afc58dac2401b41847cad39c775c64bc96f85cacb471b", "sample_id": "sim_00000005", "sample_index": 5, "scenario_key": "stdpopsim|empirical_slice|mild_noise", "seed": 2072788553, "slice_chrom": "chr17", "split": "validation"}
+{"canonical_id": "fcfc6558a872139a7f4afc58dac2401b41847cad39c775c64bc96f85cacb471b:00000006", "dataset_root": "/ibex/project/c2041/hany0c/bench_h2h_20260915/mapvar/data/v2_b_Africa_1T12__v1_true", "demography_type": "stdpopsim", "literature_model_id": "BENCH_Africa_1T12", "map_mode": "empirical_slice", "plan_sha256": "fcfc6558a872139a7f4afc58dac2401b41847cad39c775c64bc96f85cacb471b", "sample_id": "sim_00000006", "sample_index": 6, "scenario_key": "stdpopsim|empirical_slice|mild_noise", "seed": 2072796472, "slice_chrom": "chr21", "split": "validation"}
+{"canonical_id": "fcfc6558a872139a7f4afc58dac2401b41847cad39c775c64bc96f85cacb471b:00000007", "dataset_root": "/ibex/project/c2041/hany0c/bench_h2h_20260915/mapvar/data/v2_b_Africa_1T12__v1_true", "demography_type": "stdpopsim", "literature_model_id": "BENCH_Africa_1T12", "map_mode": "empirical_slice", "plan_sha256": "fcfc6558a872139a7f4afc58dac2401b41847cad39c775c64bc96f85cacb471b", "sample_id": "sim_00000007", "sample_index": 7, "scenario_key": "stdpopsim|empirical_slice|mild_noise", "seed": 2072804391, "slice_chrom": "chr8", "split": "validation"}
+{"canonical_id": "fcfc6558a872139a7f4afc58dac2401b41847cad39c775c64bc96f85cacb471b:00000008", "dataset_root": "/ibex/project/c2041/hany0c/bench_h2h_20260915/mapvar/data/v2_b_Africa_1T12__v1_true", "demography_type": "stdpopsim", "literature_model_id": "BENCH_Africa_1T12", "map_mode": "empirical_slice", "plan_sha256": "fcfc6558a872139a7f4afc58dac2401b41847cad39c775c64bc96f85cacb471b", "sample_id": "sim_00000008", "sample_index": 8, "scenario_key": "stdpopsim|empirical_slice|mild_noise", "seed": 2072812310, "slice_chrom": "chr10", "split": "train"}
+{"canonical_id": "fcfc6558a872139a7f4afc58dac2401b41847cad39c775c64bc96f85cacb471b:00000009", "dataset_root": "/ibex/project/c2041/hany0c/bench_h2h_20260915/mapvar/data/v2_b_Africa_1T12__v1_true", "demography_type": "stdpopsim", "literature_model_id": "BENCH_Africa_1T12", "map_mode": "empirical_slice", "plan_sha256": "fcfc6558a872139a7f4afc58dac2401b41847cad39c775c64bc96f85cacb471b", "sample_id": "sim_00000009", "sample_index": 9, "scenario_key": "stdpopsim|empirical_slice|mild_noise", "seed": 2072820229, "slice_chrom": "chr17", "split": "train"}
+{"canonical_id": "fcfc6558a872139a7f4afc58dac2401b41847cad39c775c64bc96f85cacb471b:00000010", "dataset_root": "/ibex/project/c2041/hany0c/bench_h2h_20260915/mapvar/data/v2_b_Africa_1T12__v1_true", "demography_type": "stdpopsim", "literature_model_id": "BENCH_Africa_1T12", "map_mode": "empirical_slice", "plan_sha256": "fcfc6558a872139a7f4afc58dac2401b41847cad39c775c64bc96f85cacb471b", "sample_id": "sim_00000010", "sample_index": 10, "scenario_key": "stdpopsim|empirical_slice|mild_noise", "seed": 2072828148, "slice_chrom": "chr21", "split": "train"}

map_variants/Africa_1T12/v1_true/necast_inputs/level32/sample_metadata.jsonl

@@ -0,0 +1,11 @@
+{"canonical_id": "fcfc6558a872139a7f4afc58dac2401b41847cad39c775c64bc96f85cacb471b:00000000", "extraction_seconds": 1.0901171043515205, "ladder_chain": 0, "ladder_columns": [39, 36, 24, 55, 28, 14, 34, 4, 30, 50, 35, 49, 33, 21, 53, 22, 45, 58, 42, 31, 6, 20, 25, 38, 27, 60, 62, 5, 3, 32, 11, 51], "ladder_level": 32, "missing_call_count": 54438, "output_index": 0, "sequence_length_bp": 30000000, "sfs_retained_site_fraction": 1.0, "source_artifact": "/ibex/project/c2041/hany0c/bench_h2h_20260915/mapvar/data/.mirrors/v2_b_Africa_1T12__v1_true/samples/.fragments/fragment_00000000.npz", "source_local_row": 0, "stream_presence": {"ibs": 1, "ld": 1, "nw": 1, "sfs": 1}, "variant_count": 58377}
+{"canonical_id": "fcfc6558a872139a7f4afc58dac2401b41847cad39c775c64bc96f85cacb471b:00000001", "extraction_seconds": 1.1198765262961388, "ladder_chain": 0, "ladder_columns": [16, 57, 22, 43, 38, 41, 39, 2, 35, 59, 51, 30, 36, 32, 40, 26, 20, 45, 47, 33, 6, 37, 34, 23, 1, 4, 58, 52, 14, 7, 49, 62], "ladder_level": 32, "missing_call_count": 128519, "output_index": 1, "sequence_length_bp": 30000000, "sfs_retained_site_fraction": 1.0, "source_artifact": "/ibex/project/c2041/hany0c/bench_h2h_20260915/mapvar/data/.mirrors/v2_b_Africa_1T12__v1_true/samples/.fragments/fragment_00000000.npz", "source_local_row": 1, "stream_presence": {"ibs": 1, "ld": 1, "nw": 1, "sfs": 1}, "variant_count": 55873}
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map_variants/Africa_1T12/v1_true/necast_inputs/level32/snapshot.json

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map_variants/Africa_1T12/v1_true/necast_inputs/psmcplus_level32/inventory.receipt.json

@@ -0,0 +1,11 @@
+{
+ "frag_dir": "/ibex/project/c2041/hany0c/bench_h2h_20260915/mapvar/data/v2_b_Africa_1T12__v1_true/samples/.fragments",
+ "fragments": 3,
+ "identities": "/ibex/project/c2041/hany0c/bench_h2h_20260915/cohort/mapvar/v2_b_Africa_1T12__v1_true/freeze/sample_identities.jsonl",
+ "identities_sha256": "c08dda7852209ba9f127b262710b227d9096aae4b911cff938ea8bbde2462f0c",
+ "inventory": "/ibex/project/c2041/hany0c/bench_h2h_20260915/cohort/mapvar/v2_b_Africa_1T12__v1_true/psmcplus_l32/inventory.npz",
+ "inventory_sha256": "6d3b5e268ad9d6d9310aee489890c61fbf672a8d5d4fa2b58dc9071217d95658",
+ "rows": 12,
+ "rows_under_500_variants": 0,
+ "variant_count_min": 55873
+}

map_variants/Africa_1T12/v1_true/necast_inputs/psmcplus_level32/resources_51966427_0.jsonl

@@ -0,0 +1,4 @@
+{"cgroup": "/sys/fs/cgroup/system.slice/slurmstepd.scope/job_51966427", "cgroup_cpu_system_s": 0.889994, "cgroup_cpu_usage_s": 3.663175, "cgroup_cpu_user_s": 2.773181, "cgroup_memory_current_bytes": 17313792, "cgroup_memory_peak_bytes": 89980928, "cpu_affinity": "6", "cpu_affinity_count": 1, "cpu_count_node": 128, "cpu_model": "AMD EPYC 7702 64-Core Processor", "cpu_models_distinct": ["AMD EPYC 7702 64-Core Processor"], "gpu_count": 0, "gpu_model": null, "gpus": null, "host": "cn113-35-l", "kind": "job_start", "label": "psmcplus:l32:v2_b_Africa_1T12__v1_true", "omp_num_threads": "1", "python": "3.9.18", "schema": "bench_h2h.resources.v1", "slurm_array_job_id": "51966427", "slurm_array_task_id": "0", "slurm_cpus_on_node": "1", "slurm_cpus_per_task": "1", "slurm_job_cpus_per_node": "1", "slurm_job_end_time": "1789587446", "slurm_job_id": "51966427", "slurm_job_name": "bench-mapvar-psmc", "slurm_job_nodelist": "cn113-35-l", "slurm_job_partition": "batch", "slurm_job_start_time": "1789578446", "slurm_mem_per_node": "12288", "start_epoch": 1789578459.4103093, "start_utc": "2026-09-16T17:07:39.410285Z", "usr_bin_time": true}
+{"cgroup": "/sys/fs/cgroup/system.slice/slurmstepd.scope/job_51966427", "cgroup_cpu_system_s": 0.9491, "cgroup_cpu_usage_s": 3.813135, "cgroup_cpu_user_s": 2.864035, "cgroup_memory_current_bytes": 17154048, "cgroup_memory_peak_bytes": 89980928, "cmd": "/home/hany0c/micromamba/envs/ctdd/bin/python -B -m bench_h2h.psmcplus_guard verify", "cpu_s": 0.072, "end_utc": "2026-09-16T17:07:39.602731Z", "exit_code": 0, "forwarded_signals": null, "gpu_names": [], "gpu_peak_memory_used_mib": null, "gpu_peak_utilization_pct": null, "gpu_sample_interval_s": null, "gpu_sampled": false, "gpu_samples": 0, "host": "cn113-35-l", "kind": "stage", "name": "psmcplus_guard", "peak_rss_kib": 19456, "peak_rss_scope": "max single process among the child and its reaped descendants (wait4)", "schema": "bench_h2h.resources.v1", "slurm_job_id": "51966427", "stage_kind": "other", "start_utc": "2026-09-16T17:07:39.510685Z", "system_cpu_s": 0.019, "term_signal": null, "user_cpu_s": 0.053, "wall_s": 0.092}
+{"cgroup": "/sys/fs/cgroup/system.slice/slurmstepd.scope/job_51966427", "cgroup_cpu_system_s": 213.718306, "cgroup_cpu_usage_s": 1479.535933, "cgroup_cpu_user_s": 1265.817627, "cgroup_memory_current_bytes": 48345088, "cgroup_memory_peak_bytes": 2241921024, "cmd": "/home/hany0c/micromamba/envs/ctdd/bin/python -B /ibex/project/c2041/hany0c/bench_h2h_20260915/tool/bench_h2h/psmcplus_l32.py 0 1 --frag-dir /ibex/project/c2041/hany0c/bench_h2h_20260915/mapvar/data/v2_b_Africa_1T12__v1_true/samples/.fragments --inventory /ibex/project/c2041/hany0c/bench_h2h_20260915/cohort/mapvar/v2_b_Africa_1T12__v1_true/psmcplus_l32/inventory.npz --out /ibex/project/c2041/hany0c/bench_h2h_20260915/cohort/mapvar/v2_b_Africa_1T12__v1_true/psmcplus_l32/store", "cpu_s": 1473.467, "end_utc": "2026-09-16T17:32:38.361011Z", "exit_code": 0, "forwarded_signals": null, "gpu_names": [], "gpu_peak_memory_used_mib": null, "gpu_peak_utilization_pct": null, "gpu_sample_interval_s": null, "gpu_sampled": false, "gpu_samples": 0, "host": "cn113-35-l", "kind": "stage", "name": "psmcplus_l32", "peak_rss_kib": 2297412, "peak_rss_scope": "max single process among the child and its reaped descendants (wait4)", "schema": "bench_h2h.resources.v1", "slurm_job_id": "51966427", "stage_kind": "preprocess", "start_utc": "2026-09-16T17:07:44.121847Z", "system_cpu_s": 212.191, "term_signal": null, "user_cpu_s": 1261.277, "wall_s": 1494.239}
+{"cgroup": "/sys/fs/cgroup/system.slice/slurmstepd.scope/job_51966427", "cgroup_cpu_system_s": 213.745166, "cgroup_cpu_usage_s": 1479.606508, "cgroup_cpu_user_s": 1265.861342, "cgroup_memory_current_bytes": 48402432, "cgroup_memory_peak_bytes": 2241921024, "end_utc": "2026-09-16T17:32:38.425944Z", "exit_code": 0, "gpu_peak_memory_used_mib": null, "host": "cn113-35-l", "job_wall_s": 1499.055, "kind": "job_end", "schema": "bench_h2h.resources.v1", "slurm_job_id": "51966427", "stages_recorded": 2}

map_variants/Africa_1T12/v1_true/necast_inputs/psmcplus_level32/store/CPU_FEATURE

@@ -0,0 +1 @@
+cpu_amd_epyc_7702

map_variants/Africa_1T12/v1_true/necast_inputs/psmcplus_level32/store/NTASK

@@ -0,0 +1 @@
+1

map_variants/Africa_1T12/v1_true/necast_inputs/psmcplus_level32/store/audit/psmcplus_00000_20260916T170743Z_1877872.json

@@ -0,0 +1,12 @@
+{
+ "opened": [
+  {
+   "mode": "r",
+   "path": "/ibex/project/c2041/hany0c/bench_h2h_20260915/cohort/mapvar/v2_b_Africa_1T12__v1_true/psmcplus_l32/inventory.npz"
+  }
+ ],
+ "purposes": [
+  "bench"
+ ],
+ "refused": []
+}

map_variants/Africa_1T12/v1_true/necast_inputs/psmcplus_level32/store/audit/psmcplus_00000_20260916T173241Z_2546679.json

@@ -0,0 +1,16 @@
+{
+ "opened": [
+  {
+   "mode": "r",
+   "path": "/ibex/project/c2041/hany0c/bench_h2h_20260915/cohort/mapvar/v2_b_Africa_1T12__v1_true/psmcplus_l32/inventory.npz"
+  },
+  {
+   "mode": "r",
+   "path": "/ibex/project/c2041/hany0c/bench_h2h_20260915/cohort/mapvar/v2_b_Africa_1T12__v1_true/psmcplus_l32/store/psmcplus_00000.npz"
+  }
+ ],
+ "purposes": [
+  "bench"
+ ],
+ "refused": []
+}

map_variants/Africa_1T12/v1_true/necast_inputs/psmcplus_level32/store/psmcplus_00000.runs.jsonl

@@ -0,0 +1 @@
+{"argv": ["/ibex/project/c2041/hany0c/bench_h2h_20260915/tool/bench_h2h/psmcplus_l32.py", "0", "1", "--frag-dir", "/ibex/project/c2041/hany0c/bench_h2h_20260915/mapvar/data/v2_b_Africa_1T12__v1_true/samples/.fragments", "--inventory", "/ibex/project/c2041/hany0c/bench_h2h_20260915/cohort/mapvar/v2_b_Africa_1T12__v1_true/psmcplus_l32/inventory.npz", "--out", "/ibex/project/c2041/hany0c/bench_h2h_20260915/cohort/mapvar/v2_b_Africa_1T12__v1_true/psmcplus_l32/store"], "audit_log": "/ibex/project/c2041/hany0c/bench_h2h_20260915/cohort/mapvar/v2_b_Africa_1T12__v1_true/psmcplus_l32/store/audit/psmcplus_00000_20260916T170745Z_1881104.json", "driver": "psmcplus_l32", "driver_sha256": "479e9110b1172161f6b97521c69572292c18efcfd2587c4781952c083a66a7d8", "env": {"SLURM_ARRAY_JOB_ID": "51966427", "SLURM_ARRAY_TASK_ID": "0", "SLURM_CPUS_PER_TASK": "1", "SLURM_JOB_ID": "51966427", "SLURM_JOB_PARTITION": "batch", "host": "cn113-35-l", "numba": "0.66.0", "numpy": "2.4.6", "pandas": "3.0.5", "prefix": "/home/hany0c/micromamba/envs/ctdd", "python": "3.11.15", "scipy": "1.17.1"}, "frag_dir": "/ibex/project/c2041/hany0c/bench_h2h_20260915/mapvar/data/v2_b_Africa_1T12__v1_true/samples/.fragments", "grid": {"dt_sha256": "97687f93838c23c7ad0fa5041616483deb760b31d02e2bee1fad9cfe245d3ec4", "edges_sha256": "0509f42cdd7b21a9cbc51077760e90c0aecffc366eba6a45ac8bfb5bb1957556"}, "import_origins": {"BaumWelch": "/ibex/project/c2041/hany0c/bench_h2h_20260915/ext/psmcplus/PSMCplus/BaumWelch.py", "dlcoal_psmcplus_sidecar": "/ibex/project/c2041/hany0c/bench_h2h_20260915/ext/psmcplus/src_20260903/training/psmcplus_sidecar.py", "ladder_spec": "/ibex/project/c2041/hany0c/bench_h2h_20260915/ext/psmcplus/ladder/ladder_spec.py", "psutil": "/ibex/project/c2041/hany0c/bench_h2h_20260915/ext/psmcplus/PSMCplus/psutil.py", "simulator": "/ibex/project/c2041/hany0c/bench_h2h_20260915/ext/psmcplus/v82/simulator/__init__.py", "simulator.config": "/ibex/project/c2041/hany0c/bench_h2h_20260915/ext/psmcplus/v82/simulator/config.py", "simulator.slurm": "/ibex/project/c2041/hany0c/bench_h2h_20260915/ext/psmcplus/v82/simulator/slurm.py", "simulator.utils": "/ibex/project/c2041/hany0c/bench_h2h_20260915/ext/psmcplus/v82/simulator/utils.py", "transition_matrix": "/ibex/project/c2041/hany0c/bench_h2h_20260915/ext/psmcplus/PSMCplus/transition_matrix.py", "utils": "/ibex/project/c2041/hany0c/bench_h2h_20260915/ext/psmcplus/PSMCplus/utils.py"}, "inventory": "/ibex/project/c2041/hany0c/bench_h2h_20260915/cohort/mapvar/v2_b_Africa_1T12__v1_true/psmcplus_l32/inventory.npz", "inventory_sha256": "6d3b5e268ad9d6d9310aee489890c61fbf672a8d5d4fa2b58dc9071217d95658", "numba": "0.66.0", "only_chain": 0, "only_level": 32, "originals_checked": true, "out": "/ibex/project/c2041/hany0c/bench_h2h_20260915/cohort/mapvar/v2_b_Africa_1T12__v1_true/psmcplus_l32/store", "tmpdir": "/ibex/project/c2041/hany0c/bench_h2h_20260915/tmp/psmcplus/51966427_0_r0/psmcladder_d0gtju0x", "utc": "2026-09-16T17:07:45Z", "vendor_table_sha256": "ce095acef7b10655ef1ad8c506f7b4eb6fca1851562df01a0e46ab1053ac2592"}

map_variants/Africa_1T12/v1_true/necast_inputs/psmcplus_posterior/level32.receipt.json

@@ -0,0 +1,36 @@
+{
+ "absent": 0,
+ "array_sha256": {
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+ },
+ "cache": "/ibex/project/c2041/hany0c/bench_h2h_20260915/cohort/mapvar/v2_b_Africa_1T12__v1_true/chain0_level32/unphased_evidence_cache.npz",
+ "cache_sample_metadata_sha256": "ace3342063e24b382707ac28e5d12bcd87d36e1e03dfb7ca0f52cecc4ac3c9e2",
+ "cache_sha256": "a3b0a2db12f8f8d7bd2102d0efd759d1fe80747bb14c5e067d9872d41e6b0f44",
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+ "ladder_columns_bound_to_ladder_spec": true,
+ "level": 32,
+ "missing_examples": [],
+ "missing_from_store": 0,
+ "nonfinite_values_zeroed": 0,
+ "out": "/ibex/project/c2041/hany0c/bench_h2h_20260915/cohort/mapvar/v2_b_Africa_1T12__v1_true/sidecar/chain0_level32.npz",
+ "out_sha256": "5c76a919404a776929de2a724d2125ab1c0f86dad501b9dbaab9336d1e5c7f6d",
+ "present": 11,
+ "rows": 11,
+ "rows_under_500_variants": 0,
+ "rows_with_features": 11,
+ "semantics": "make_sidecar_109k.py (sha 74b51a58): present = n_scored_plain > 0 & seen; non-finite -> 0; < 500 variants -> absent; cache order; join on canonical_id",
+ "store_rows": 12,
+ "store_rows_not_in_cache": 1,
+ "store_shards": [
+  [
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+   "6aa20f38d65b9ade07bad9e3b15fa63de0734ad751e6ffb057b36f802258d816"
+  ]
+ ],
+ "utc": "2026-09-16T18:12:55Z",
+ "width": 256
+}

map_variants/Africa_1T12/v1_true/necast_inputs/registry/DONE.json

@@ -0,0 +1,9 @@
+{
+  "all_raw_roundtrips_passed": true,
+  "raw_index_sha256": "738419c6df6700bb6e11bf83ce31b2736fc31ddb33eb5a0cccb73a7b8da89691",
+  "report_sha256": "6c4b2dffc20e25fdddb295d1319c1b85962d550ae0426e8a6e104d82e5ff3fb2",
+  "schema": "dlcoalsim-lossless-raw-site-index-v1",
+  "schema_version": 1,
+  "selected_samples": 11,
+  "status": "complete"
+}

map_variants/Africa_1T12/v1_true/necast_inputs/registry/PLAN.json

@@ -0,0 +1,67 @@
+{
+  "architecture_split_sha256": "7fc3c7f026176332e7a7b92f7a1a9c8bcfc168e76fbac8015dcdbb9f1166bf9c",
+  "builder_deployment": null,
+  "command": [
+    "/ibex/project/c2041/hany0c/deploy_20260913_fixed32/training/raw_site_gate.py",
+    "--snapshot",
+    "/ibex/project/c2041/hany0c/bench_h2h_20260915/cohort/mapvar/v2_b_Africa_1T12__v1_true/freeze/snapshot.json",
+    "--reference-cache",
+    "/ibex/project/c2041/hany0c/bench_h2h_20260915/cohort/mapvar/v2_b_Africa_1T12__v1_true/freeze/reference_cache.npz",
+    "--identities",
+    "/ibex/project/c2041/hany0c/bench_h2h_20260915/cohort/mapvar/v2_b_Africa_1T12__v1_true/freeze/sample_identities.jsonl",
+    "--architecture-split",
+    "/ibex/project/c2041/hany0c/bench_h2h_20260915/cohort/mapvar/v2_b_Africa_1T12__v1_true/freeze/architecture_split.jsonl",
+    "--out-dir",
+    "/ibex/project/c2041/hany0c/bench_h2h_20260915/cohort/mapvar/v2_b_Africa_1T12__v1_true/registry",
+    "--gate-samples",
+    "11",
+    "--source-root-map",
+    "/ibex/project/c2041/hany0c/bench_h2h_20260915/mapvar/data/v2_b_Africa_1T12__v1_true=/ibex/project/c2041/hany0c/bench_h2h_20260915/mapvar/data/.mirrors/v2_b_Africa_1T12__v1_true"
+  ],
+  "identities_sha256": "c08dda7852209ba9f127b262710b227d9096aae4b911cff938ea8bbde2462f0c",
+  "observation_schema": "uint32-position-uint8-packed128-sparse-missing-exact-v1",
+  "physical_source_root_map": {
+    "/ibex/project/c2041/hany0c/bench_h2h_20260915/mapvar/data/v2_b_Africa_1T12__v1_true": "/ibex/project/c2041/hany0c/bench_h2h_20260915/mapvar/data/.mirrors/v2_b_Africa_1T12__v1_true"
+  },
+  "reference_cache": "/ibex/project/c2041/hany0c/bench_h2h_20260915/cohort/mapvar/v2_b_Africa_1T12__v1_true/freeze/reference_cache.npz",
+  "reference_cache_sha256": "3d7f402c29bd32b8907ed13d78daabc08b4938de1a3b641e16567f8237ef98de",
+  "runtime_source_sha256": {
+    "training/data.py": "8a2b675099368f3758a542f5452edbad4433da3685af4afefdce2d7350bc9ebd",
+    "training/ibs_tract_cache.py": "d1da91b2a08a8ddf3cfb8929e7328ae009e929057e7f10943b5a7ba0afe5d42d",
+    "training/raw_site_gate.py": "0741bfaa9e72dcdda26eca236ae93a4f605a61e5ae1d2b2da5b1aed63772d0fd",
+    "training/sfs_context_cache.py": "db9cad0dbce9b357507e2525b95c1658f55d9552e7bdf524cad09a3ecedf4151"
+  },
+  "schema": "dlcoalsim-lossless-raw-site-index-v1",
+  "schema_version": 1,
+  "scientific_semantics": {
+    "forbidden_heads": [
+      "hazard",
+      "tail",
+      "survival",
+      "dual demography",
+      "class label"
+    ],
+    "forbidden_preprocessing": [
+      "site thinning",
+      "top-k",
+      "site subsampling",
+      "Fourier projection",
+      "dense fixed-site cache"
+    ],
+    "fourier_backprojection": {
+      "implemented": false,
+      "reason": "the existing 19-channel irregular-site Fourier moment map is non-injective and has no unique binary/missing-aware inverse; an arbitrary pseudoinverse would be a fabricated scientific mechanism"
+    },
+    "losslessness_scope": "input/storage only; the learned 100 bp-to-1 Mb latent pyramid is deliberately not invertible",
+    "missing_policy": "packed simulator bits are retained for byte audit but a downstream model must erase alleles at missing calls",
+    "representation": "index-only exact persisted raw positions, packed 64-haplotype calls and sparse missing calls",
+    "targets": "direct 64 log10-Ne bins only"
+  },
+  "selected_samples": 11,
+  "selection_excluded_before_raw_task_construction": true,
+  "selection_rows_excluded_before_variant_count_access": 1,
+  "snapshot": "/ibex/project/c2041/hany0c/bench_h2h_20260915/cohort/mapvar/v2_b_Africa_1T12__v1_true/freeze/snapshot.json",
+  "snapshot_sha256": "0d3fd70d6751861ce9af11de6f34578de363255d061c8230b849e0346f1de207",
+  "status": "indexing",
+  "verify_source_sha256": true
+}

map_variants/Africa_1T12/v1_true/necast_inputs/registry/architecture_split.jsonl

@@ -0,0 +1,11 @@
+{"architecture_group": "bench:fcfc6558a872139a7f4afc58dac2401b41847cad39c775c64bc96f85cacb471b:00000000", "canonical_id": "fcfc6558a872139a7f4afc58dac2401b41847cad39c775c64bc96f85cacb471b:00000000", "seed": 2072748958, "split": "validation"}
+{"architecture_group": "bench:fcfc6558a872139a7f4afc58dac2401b41847cad39c775c64bc96f85cacb471b:00000001", "canonical_id": "fcfc6558a872139a7f4afc58dac2401b41847cad39c775c64bc96f85cacb471b:00000001", "seed": 2072756877, "split": "validation"}
+{"architecture_group": "bench:fcfc6558a872139a7f4afc58dac2401b41847cad39c775c64bc96f85cacb471b:00000002", "canonical_id": "fcfc6558a872139a7f4afc58dac2401b41847cad39c775c64bc96f85cacb471b:00000002", "seed": 2072764796, "split": "validation"}
+{"architecture_group": "bench:fcfc6558a872139a7f4afc58dac2401b41847cad39c775c64bc96f85cacb471b:00000003", "canonical_id": "fcfc6558a872139a7f4afc58dac2401b41847cad39c775c64bc96f85cacb471b:00000003", "seed": 2072772715, "split": "validation"}
+{"architecture_group": "bench:fcfc6558a872139a7f4afc58dac2401b41847cad39c775c64bc96f85cacb471b:00000004", "canonical_id": "fcfc6558a872139a7f4afc58dac2401b41847cad39c775c64bc96f85cacb471b:00000004", "seed": 2072780634, "split": "validation"}
+{"architecture_group": "bench:fcfc6558a872139a7f4afc58dac2401b41847cad39c775c64bc96f85cacb471b:00000005", "canonical_id": "fcfc6558a872139a7f4afc58dac2401b41847cad39c775c64bc96f85cacb471b:00000005", "seed": 2072788553, "split": "validation"}
+{"architecture_group": "bench:fcfc6558a872139a7f4afc58dac2401b41847cad39c775c64bc96f85cacb471b:00000006", "canonical_id": "fcfc6558a872139a7f4afc58dac2401b41847cad39c775c64bc96f85cacb471b:00000006", "seed": 2072796472, "split": "validation"}
+{"architecture_group": "bench:fcfc6558a872139a7f4afc58dac2401b41847cad39c775c64bc96f85cacb471b:00000007", "canonical_id": "fcfc6558a872139a7f4afc58dac2401b41847cad39c775c64bc96f85cacb471b:00000007", "seed": 2072804391, "split": "validation"}
+{"architecture_group": "bench:fcfc6558a872139a7f4afc58dac2401b41847cad39c775c64bc96f85cacb471b:00000008", "canonical_id": "fcfc6558a872139a7f4afc58dac2401b41847cad39c775c64bc96f85cacb471b:00000008", "seed": 2072812310, "split": "train"}
+{"architecture_group": "bench:fcfc6558a872139a7f4afc58dac2401b41847cad39c775c64bc96f85cacb471b:00000009", "canonical_id": "fcfc6558a872139a7f4afc58dac2401b41847cad39c775c64bc96f85cacb471b:00000009", "seed": 2072820229, "split": "train"}
+{"architecture_group": "bench:fcfc6558a872139a7f4afc58dac2401b41847cad39c775c64bc96f85cacb471b:00000010", "canonical_id": "fcfc6558a872139a7f4afc58dac2401b41847cad39c775c64bc96f85cacb471b:00000010", "seed": 2072828148, "split": "train"}

map_variants/Africa_1T12/v1_true/necast_inputs/registry/gate.json

@@ -0,0 +1,38 @@
+{
+  "eligible_development_samples": 11,
+  "logical_root_counts": {
+    "/ibex/project/c2041/hany0c/bench_h2h_20260915/mapvar/data/v2_b_Africa_1T12__v1_true": 11
+  },
+  "requested_samples": 11,
+  "schema": "dlcoal-ibs-tract-extreme-balanced-gate-v1",
+  "sealed_selection_samples_excluded_before_ranking": 1,
+  "selected_rows": [
+    0,
+    1,
+    2,
+    3,
+    4,
+    5,
+    6,
+    7,
+    8,
+    9,
+    10
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+  "selected_variant_counts": [
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+    61594,
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+    56515,
+    61129,
+    67362,
+    60817
+  ],
+  "selection": "balance logical dataset_root; alternate smallest/largest exact variant count; canonical_id tie break; publish reference row order",
+  "variant_count_max": 71263,
+  "variant_count_min": 55873
+}

map_variants/Africa_1T12/v1_true/necast_inputs/registry/raw_index.jsonl

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map_variants/Africa_1T12/v1_true/necast_inputs/registry/report.json

@@ -0,0 +1,82 @@
+{
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+    "/ibex/project/c2041/hany0c/bench_h2h_20260915/cohort/mapvar/v2_b_Africa_1T12__v1_true/freeze/snapshot.json",
+    "--reference-cache",
+    "/ibex/project/c2041/hany0c/bench_h2h_20260915/cohort/mapvar/v2_b_Africa_1T12__v1_true/freeze/reference_cache.npz",
+    "--identities",
+    "/ibex/project/c2041/hany0c/bench_h2h_20260915/cohort/mapvar/v2_b_Africa_1T12__v1_true/freeze/sample_identities.jsonl",
+    "--architecture-split",
+    "/ibex/project/c2041/hany0c/bench_h2h_20260915/cohort/mapvar/v2_b_Africa_1T12__v1_true/freeze/architecture_split.jsonl",
+    "--out-dir",
+    "/ibex/project/c2041/hany0c/bench_h2h_20260915/cohort/mapvar/v2_b_Africa_1T12__v1_true/registry",
+    "--gate-samples",
+    "11",
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+    "/ibex/project/c2041/hany0c/bench_h2h_20260915/mapvar/data/v2_b_Africa_1T12__v1_true=/ibex/project/c2041/hany0c/bench_h2h_20260915/mapvar/data/.mirrors/v2_b_Africa_1T12__v1_true"
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+  },
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+  "raw_index": "raw_index.jsonl",
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+    "training/sfs_context_cache.py": "db9cad0dbce9b357507e2525b95c1658f55d9552e7bdf524cad09a3ecedf4151"
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+  "schema": "dlcoalsim-lossless-raw-site-index-v1",
+  "schema_version": 1,
+  "scientific_semantics": {
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+      "survival",
+      "dual demography",
+      "class label"
+    ],
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+      "site thinning",
+      "top-k",
+      "site subsampling",
+      "Fourier projection",
+      "dense fixed-site cache"
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+    "fourier_backprojection": {
+      "implemented": false,
+      "reason": "the existing 19-channel irregular-site Fourier moment map is non-injective and has no unique binary/missing-aware inverse; an arbitrary pseudoinverse would be a fabricated scientific mechanism"
+    },
+    "losslessness_scope": "input/storage only; the learned 100 bp-to-1 Mb latent pyramid is deliberately not invertible",
+    "missing_policy": "packed simulator bits are retained for byte audit but a downstream model must erase alleles at missing calls",
+    "representation": "index-only exact persisted raw positions, packed 64-haplotype calls and sparse missing calls",
+    "targets": "direct 64 log10-Ne bins only"
+  },
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+  "selected_samples": 11,
+  "selection_excluded_before_raw_task_construction": true,
+  "selection_rows_excluded_before_variant_count_access": 1,
+  "snapshot": "/ibex/project/c2041/hany0c/bench_h2h_20260915/cohort/mapvar/v2_b_Africa_1T12__v1_true/freeze/snapshot.json",
+  "snapshot_sha256": "0d3fd70d6751861ce9af11de6f34578de363255d061c8230b849e0346f1de207",
+  "status": "complete",
+  "variant_count_summary": {
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+    "median": 60817.0,
+    "min": 55873
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+  "verify_source_sha256": true
+}

map_variants/Africa_1T12/v1_true/necast_inputs/registry/sample_identities.jsonl

@@ -0,0 +1,11 @@
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map_variants/Africa_1T12/v1_true/necast_inputs/registry/snapshot.json

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map_variants/Africa_1T12/v1_true/windows/MAPVAR_ROWS.json

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map_variants/Africa_1T12/v1_true/windows/samples/fragments/fragment_00000000.done.json

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map_variants/Africa_1T12/v1_true/windows/samples/fragments/fragment_00000002.done.json

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map_variants/Africa_1T12/v3_flat_genomewide/estimates/audit-compare-51974588.json

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map_variants/Africa_1T12/v3_flat_genomewide/estimates/compare_source_final_51974588.json

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map_variants/Africa_1T12/v3_flat_genomewide/estimates/final/SCORE_MANIFEST.json

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+}

map_variants/Africa_1T12/v3_flat_genomewide/estimates/t0_final_51974588.json

@@ -0,0 +1,102 @@
+{
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+}

map_variants/Africa_1T12/v3_flat_genomewide/necast_inputs/COHORT_RECEIPT.json

@@ -0,0 +1,45 @@
+{
+ "cohort": "/ibex/project/c2041/hany0c/bench_h2h_20260915/cohort/mapvar/v2_b_Africa_1T12__v3_flat_genomewide",
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+ "source_cohort": "/ibex/project/c2041/hany0c/bench_h2h_20260915/cohort/v2_b_Africa_1T12",
+ "variant": "v3_flat_genomewide"
+}

map_variants/Africa_1T12/v3_flat_genomewide/necast_inputs/freeze/architecture_split.jsonl

@@ -0,0 +1,12 @@
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+{"architecture_group": "bench:cc91d714c51d1e892fe9057d31880d8dbfb50a3b8a8079649ca470aa9a4b9c76:00000003", "canonical_id": "cc91d714c51d1e892fe9057d31880d8dbfb50a3b8a8079649ca470aa9a4b9c76:00000003", "seed": 2072772715, "split": "validation"}
+{"architecture_group": "bench:cc91d714c51d1e892fe9057d31880d8dbfb50a3b8a8079649ca470aa9a4b9c76:00000004", "canonical_id": "cc91d714c51d1e892fe9057d31880d8dbfb50a3b8a8079649ca470aa9a4b9c76:00000004", "seed": 2072780634, "split": "validation"}
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map_variants/Africa_1T12/v3_flat_genomewide/necast_inputs/freeze/open_audit.json

@@ -0,0 +1,94 @@
+{
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+  },
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+  },
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map_variants/Africa_1T12/v3_flat_genomewide/necast_inputs/freeze/report.json

@@ -0,0 +1,175 @@
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map_variants/Africa_1T12/v3_flat_genomewide/necast_inputs/freeze/sample_identities.jsonl

@@ -0,0 +1,12 @@
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map_variants/Africa_1T12/v3_flat_genomewide/necast_inputs/freeze/snapshot.json

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