P2_MDD_CON_SEURAT_UPSTREAM_DUAL_GRAPH_BUILD

Review state: WAITING_FOR_INVESTIGATOR_REVIEW. test_only=False.

Objective

On the preflight-validated 625220/70 universe, freeze consensus HVG, ScaleData, PCA 100, seal uncorrected primary NN/SNN, run Harmony(Channel) sensitivity, seal sensitivity NN/SNN. Do not cluster.

Scientific scope

['reuse preflight-validated load identities', 'single LogNormalize', 'sequential Channel VST 2000 on eligible-only temp objects and SelectIntegrationFeatures 2000', 'ScaleData on frozen HVG', 'RunPCA npcs=100', 'primary uncorrected PCA graphs sealed before Harmony', 'Harmony(Channel) on PC 1:30 via exported harmony::RunHarmony', 'sensitivity graphs', 'resource and parameter logging']

Out of scope

['clustering', 'resolution', 'UMAP parameter selection', 'annotation', 'Ast membership freeze', 'pseudobulk', 'DE', 'pathway', 'PTSD/105-Channel fit', 'diagnosis reads', 'reuse of b0780b59-f106-4e0a-8795-12790307aab0', 'VST on all 27982 genes then post-filter']

Identity

task_id 5792cc3d-0a4b-4880-ac51-e7cb304e6954
contract_body_sha256 103fc8ffcd90105b50606295bc5b14e65cc7da8357214aa209c7ae3f9d99280f
execution runtime release_id Seurat-5.3.0-harmony-1.2.4-R-4.5.1-QUALIFICATION_TARGET
runtime_manifest_sha256
cloud environment hash
Record checkpoint
review schema p2.contract_review_projection.v1
method identity p2-upstream-dual-graph/v1.1b

Resolved inputs

asset	role	replica	sha256	status
P2 计数矩阵（只公布逻辑名与哈希）	counts	SSH_CLOUD	79876eda346f3a6c325a2cb33de9f35cfc2d276018b79462bd749a957b279922	DECLARED
P2 细胞序	cell_order	SSH_CLOUD	3d274bcc16ef0d57014e4c2a47bf47e7f83bdf579f2fc8d8be349c17a9b7a9ba	DECLARED
P2 基因序	gene_order	SSH_CLOUD	ba827830af502d16a9aa4dbc80a31bb61bc5b7ec440698171d78bfc5af1fee62	DECLARED
P2 MDD+CON 聚类队列（625,220 / 70 Channels）	universe	SSH_CLOUD	ffc9dcc707452e5b49ebd12132d3b2bff2143b1871bb59bbb1f45536bcd1e3f4	DECLARED
P2 RNA 基因身份台账	gene_identity	SSH_CLOUD	30daac6ee5a4319f6c1483227ec6b1af75bcadbb5b5e66f0ca8536793a5b6997	DECLARED

Scientific parameters

{
  "counts_layer_digest": "120cf48fb8bd237200b0e464a7defc9b964925e3f0c93ad063dc00004565f91f",
  "dims": "1:30",
  "harmony_call": "harmony::RunHarmony(data_mat, meta_data, vars_use, theta, sigma, lambda, nclust, max_iter, early_stop, ncores, plot_convergence, return_object, verbose, .options)",
  "k_param": 30,
  "n_channel": 70,
  "n_genes": 27982,
  "n_nuclei": 625220,
  "nclust": 100,
  "pca_npcs": 100,
  "plot_convergence": false,
  "primary": "uncorrected PCA graph",
  "requested_theta": null,
  "sensitivity": "Harmony(Channel)",
  "subset_nnz": 1875045667,
  "umi_global": 5630250337
}

Acceptance criteria

five input SHA256 MATCH
counts_layer_digest MATCH
UMI 5630250337
PCA 100 / graphs and Harmony 1:30 / k.param 30
call exported harmony::RunHarmony; do not call harmony::RunHarmony.default or RunHarmony.Seurat
SCIENTIFIC_GO remains false until separate execution approval

HOLD / stop

canonical_stop=WAITING_FOR_INVESTIGATOR_REVIEW

input SHA256, cell order/set, Channel join, gene order, dimensions, nnz, or UMI mismatch
counts_layer_digest mismatch or Seurat @x storage mutated: HOLD_COUNTS_LAYER_MUTATED
VST not eligible-only first, or Channel/consensus HVG is not 2000 unique eligible features
PCA is not 100, graphs/Harmony leave 1:30, graph names overwrite, or primary is not sealed first
Harmony error, nonzero status, user stop, or no confirmed convergence: keep sealed primary, dual-graph delivery HOLD, do not add iterations
OOM, disk, checkpoint failure, or 70 full objects coresident
clustering, resolution, UMAP, annotation, Ast membership, pseudobulk, DE, or diagnosis use

Outputs

not declared

Machine-readable sources: projection.json · contract.json · manifest.json

Technical JSON (same objects as the files above)

{
  "contract": {
    "acceptance_criteria": [
      "five input SHA256 MATCH",
      "counts_layer_digest MATCH",
      "UMI 5630250337",
      "PCA 100 / graphs and Harmony 1:30 / k.param 30",
      "call exported harmony::RunHarmony; do not call harmony::RunHarmony.default or RunHarmony.Seurat",
      "SCIENTIFIC_GO remains false until separate execution approval"
    ],
    "canonical_stop": "WAITING_FOR_INVESTIGATOR_REVIEW",
    "cloud_environment_manifest_sha256": null,
    "contract_body_sha256": "103fc8ffcd90105b50606295bc5b14e65cc7da8357214aa209c7ae3f9d99280f",
    "excluded_scope": [
      "clustering",
      "resolution",
      "UMAP parameter selection",
      "annotation",
      "Ast membership freeze",
      "pseudobulk",
      "DE",
      "pathway",
      "PTSD/105-Channel fit",
      "diagnosis reads",
      "reuse of b0780b59-f106-4e0a-8795-12790307aab0",
      "VST on all 27982 genes then post-filter"
    ],
    "execution_runtime_release_id": "Seurat-5.3.0-harmony-1.2.4-R-4.5.1-QUALIFICATION_TARGET",
    "holds": [
      "input SHA256, cell order/set, Channel join, gene order, dimensions, nnz, or UMI mismatch",
      "counts_layer_digest mismatch or Seurat @x storage mutated: HOLD_COUNTS_LAYER_MUTATED",
      "VST not eligible-only first, or Channel/consensus HVG is not 2000 unique eligible features",
      "PCA is not 100, graphs/Harmony leave 1:30, graph names overwrite, or primary is not sealed first",
      "Harmony error, nonzero status, user stop, or no confirmed convergence: keep sealed primary, dual-graph delivery HOLD, do not add iterations",
      "OOM, disk, checkpoint failure, or 70 full objects coresident",
      "clustering, resolution, UMAP, annotation, Ast membership, pseudobulk, DE, or diagnosis use"
    ],
    "method_identity": "p2-upstream-dual-graph/v1.1b",
    "objective": "On the preflight-validated 625220/70 universe, freeze consensus HVG, ScaleData, PCA 100, seal uncorrected primary NN/SNN, run Harmony(Channel) sensitivity, seal sensitivity NN/SNN. Do not cluster.",
    "output_assets": [],
    "parent_contract_body_sha256": "83bde8a9fb9eb4a853d10b7b9170a02bc1ffd83dd9a25af3bcdda36679387e10",
    "project_id": "MDD_DLPFC_ANALYSIS_WORKSPACE",
    "record_checkpoint_id": null,
    "resolved_inputs": [
      {
        "alias_zh": "P2 计数矩阵（只公布逻辑名与哈希）",
        "asset_id": "P2_CSR_COUNT_MATRIX",
        "execution_location": "cloud",
        "path_withheld": true,
        "restricted": false,
        "role": "counts",
        "selected_replica": "SSH_CLOUD",
        "sha256": "79876eda346f3a6c325a2cb33de9f35cfc2d276018b79462bd749a957b279922",
        "status": "DECLARED"
      },
      {
        "alias_zh": "P2 细胞序",
        "asset_id": "P2_RNA_CELLNAMES",
        "execution_location": "cloud",
        "path_withheld": true,
        "restricted": false,
        "role": "cell_order",
        "selected_replica": "SSH_CLOUD",
        "sha256": "3d274bcc16ef0d57014e4c2a47bf47e7f83bdf579f2fc8d8be349c17a9b7a9ba",
        "status": "DECLARED"
      },
      {
        "alias_zh": "P2 基因序",
        "asset_id": "P2_RNA_GENENAMES",
        "execution_location": "cloud",
        "path_withheld": true,
        "restricted": false,
        "role": "gene_order",
        "selected_replica": "SSH_CLOUD",
        "sha256": "ba827830af502d16a9aa4dbc80a31bb61bc5b7ec440698171d78bfc5af1fee62",
        "status": "DECLARED"
      },
      {
        "alias_zh": "P2 MDD+CON 聚类队列（625,220 / 70 Channels）",
        "asset_id": "P2_MDD_CON_CLUSTERING_COHORT_625220",
        "execution_location": "cloud",
        "path_withheld": true,
        "restricted": false,
        "role": "universe",
        "selected_replica": "SSH_CLOUD",
        "sha256": "ffc9dcc707452e5b49ebd12132d3b2bff2143b1871bb59bbb1f45536bcd1e3f4",
        "status": "DECLARED"
      },
      {
        "alias_zh": "P2 RNA 基因身份台账",
        "asset_id": "P2_RNA_GENE_IDENTITY_LEDGER",
        "execution_location": "cloud",
        "path_withheld": true,
        "restricted": false,
        "role": "gene_identity",
        "selected_replica": "SSH_CLOUD",
        "sha256": "30daac6ee5a4319f6c1483227ec6b1af75bcadbb5b5e66f0ca8536793a5b6997",
        "status": "DECLARED"
      }
    ],
    "review_schema": "p2.contract_review_projection.v1",
    "runtime_manifest_sha256": null,
    "schema": "p2.review_public_contract.v1",
    "schema_version": "p2.upstream_dual_graph_execution_contract_candidate.v1.1b",
    "scientific_go": false,
    "scientific_parameters": {
      "counts_layer_digest": "120cf48fb8bd237200b0e464a7defc9b964925e3f0c93ad063dc00004565f91f",
      "dims": "1:30",
      "harmony_call": "harmony::RunHarmony(data_mat, meta_data, vars_use, theta, sigma, lambda, nclust, max_iter, early_stop, ncores, plot_convergence, return_object, verbose, .options)",
      "k_param": 30,
      "n_channel": 70,
      "n_genes": 27982,
      "n_nuclei": 625220,
      "nclust": 100,
      "pca_npcs": 100,
      "plot_convergence": false,
      "primary": "uncorrected PCA graph",
      "requested_theta": null,
      "sensitivity": "Harmony(Channel)",
      "subset_nnz": 1875045667,
      "umi_global": 5630250337
    },
    "scientific_scope": [
      "reuse preflight-validated load identities",
      "single LogNormalize",
      "sequential Channel VST 2000 on eligible-only temp objects and SelectIntegrationFeatures 2000",
      "ScaleData on frozen HVG",
      "RunPCA npcs=100",
      "primary uncorrected PCA graphs sealed before Harmony",
      "Harmony(Channel) on PC 1:30 via exported harmony::RunHarmony",
      "sensitivity graphs",
      "resource and parameter logging"
    ],
    "task_id": "5792cc3d-0a4b-4880-ac51-e7cb304e6954",
    "test_only": false,
    "title": "P2_MDD_CON_SEURAT_UPSTREAM_DUAL_GRAPH_BUILD",
    "webpage_is_not_scientific_authorization": true
  },
  "projection": {
    "acceptance_criteria": [
      "five input SHA256 MATCH",
      "counts_layer_digest MATCH",
      "UMI 5630250337",
      "PCA 100 / graphs and Harmony 1:30 / k.param 30",
      "call exported harmony::RunHarmony; do not call harmony::RunHarmony.default or RunHarmony.Seurat",
      "SCIENTIFIC_GO remains false until separate execution approval"
    ],
    "approval_requirement": {
      "authorized_scientific_step": "P2_UPSTREAM_DUAL_GRAPH",
      "channel": "existing trusted approval envelope; not this webpage",
      "required": true
    },
    "contract_body_sha256": "103fc8ffcd90105b50606295bc5b14e65cc7da8357214aa209c7ae3f9d99280f",
    "contract_frozen_at": "2026-09-25T11:08:36.415308Z",
    "excluded_scope": [
      "clustering",
      "resolution",
      "UMAP parameter selection",
      "annotation",
      "Ast membership freeze",
      "pseudobulk",
      "DE",
      "pathway",
      "PTSD/105-Channel fit",
      "diagnosis reads",
      "reuse of b0780b59-f106-4e0a-8795-12790307aab0",
      "VST on all 27982 genes then post-filter"
    ],
    "execution_location": "cloud",
    "expected_outputs": [
      "HVG_FREEZE",
      "primary_nn/primary_snn",
      "harmony_channel",
      "harmony_channel_nn/harmony_channel_snn",
      "resource log"
    ],
    "frozen_contract_hash": "103fc8ffcd90105b50606295bc5b14e65cc7da8357214aa209c7ae3f9d99280f",
    "holds": [
      "input SHA256, cell order/set, Channel join, gene order, dimensions, nnz, or UMI mismatch",
      "counts_layer_digest mismatch or Seurat @x storage mutated: HOLD_COUNTS_LAYER_MUTATED",
      "VST not eligible-only first, or Channel/consensus HVG is not 2000 unique eligible features",
      "PCA is not 100, graphs/Harmony leave 1:30, graph names overwrite, or primary is not sealed first",
      "Harmony error, nonzero status, user stop, or no confirmed convergence: keep sealed primary, dual-graph delivery HOLD, do not add iterations",
      "OOM, disk, checkpoint failure, or 70 full objects coresident",
      "clustering, resolution, UMAP, annotation, Ast membership, pseudobulk, DE, or diagnosis use"
    ],
    "kind": "PRE_EXECUTION_REVIEW",
    "loop": "0.3.2-rc4",
    "not_a_commit": true,
    "not_a_scientific_result": true,
    "objective": "On the preflight-validated 625220/70 universe, freeze consensus HVG, ScaleData, PCA 100, seal uncorrected primary NN/SNN, run Harmony(Channel) sensitivity, seal sensitivity NN/SNN. Do not cluster.",
    "policy_summary": "execution_location=cloud; call harmony::RunHarmony; Seurat 5.3.0 / harmony 1.2.4 / R 4.5.1 qualification target; not Pegasus ACTIVE release; Worker not started; freeze_id is not a registered execution task",
    "project_id": "MDD_DLPFC_ANALYSIS_WORKSPACE",
    "resolved_logical_assets": [
      {
        "alias_zh": "P2 计数矩阵（只公布逻辑名与哈希）",
        "asset_id": "P2_CSR_COUNT_MATRIX",
        "execution_location": "cloud",
        "path_withheld": true,
        "restricted": false,
        "role": "counts",
        "selected_replica": "SSH_CLOUD",
        "sha256": "79876eda346f3a6c325a2cb33de9f35cfc2d276018b79462bd749a957b279922",
        "status": "DECLARED"
      },
      {
        "alias_zh": "P2 细胞序",
        "asset_id": "P2_RNA_CELLNAMES",
        "execution_location": "cloud",
        "path_withheld": true,
        "restricted": false,
        "role": "cell_order",
        "selected_replica": "SSH_CLOUD",
        "sha256": "3d274bcc16ef0d57014e4c2a47bf47e7f83bdf579f2fc8d8be349c17a9b7a9ba",
        "status": "DECLARED"
      },
      {
        "alias_zh": "P2 基因序",
        "asset_id": "P2_RNA_GENENAMES",
        "execution_location": "cloud",
        "path_withheld": true,
        "restricted": false,
        "role": "gene_order",
        "selected_replica": "SSH_CLOUD",
        "sha256": "ba827830af502d16a9aa4dbc80a31bb61bc5b7ec440698171d78bfc5af1fee62",
        "status": "DECLARED"
      },
      {
        "alias_zh": "P2 MDD+CON 聚类队列（625,220 / 70 Channels）",
        "asset_id": "P2_MDD_CON_CLUSTERING_COHORT_625220",
        "execution_location": "cloud",
        "path_withheld": true,
        "restricted": false,
        "role": "universe",
        "selected_replica": "SSH_CLOUD",
        "sha256": "ffc9dcc707452e5b49ebd12132d3b2bff2143b1871bb59bbb1f45536bcd1e3f4",
        "status": "DECLARED"
      },
      {
        "alias_zh": "P2 RNA 基因身份台账",
        "asset_id": "P2_RNA_GENE_IDENTITY_LEDGER",
        "execution_location": "cloud",
        "path_withheld": true,
        "restricted": false,
        "role": "gene_identity",
        "selected_replica": "SSH_CLOUD",
        "sha256": "30daac6ee5a4319f6c1483227ec6b1af75bcadbb5b5e66f0ca8536793a5b6997",
        "status": "DECLARED"
      }
    ],
    "review_snapshot_id": "rev-5792cc3d-0a4b-4880-ac51-e7cb304e6954-103fc8ffcd90",
    "review_state": "WAITING_FOR_INVESTIGATOR_REVIEW",
    "reviewed_contract_hash": "103fc8ffcd90105b50606295bc5b14e65cc7da8357214aa209c7ae3f9d99280f",
    "schema": "p2.contract_review_projection.v1",
    "scientific_go": false,
    "scientific_scope": [
      "reuse preflight-validated load identities",
      "single LogNormalize",
      "sequential Channel VST 2000 on eligible-only temp objects and SelectIntegrationFeatures 2000",
      "ScaleData on frozen HVG",
      "RunPCA npcs=100",
      "primary uncorrected PCA graphs sealed before Harmony",
      "Harmony(Channel) on PC 1:30 via exported harmony::RunHarmony",
      "sensitivity graphs",
      "resource and parameter logging"
    ],
    "scientific_step": "P2_UPSTREAM_DUAL_GRAPH",
    "task_id": "5792cc3d-0a4b-4880-ac51-e7cb304e6954",
    "task_title": "P2_MDD_CON_SEURAT_UPSTREAM_DUAL_GRAPH_BUILD",
    "test_only": false,
    "webpage_is_not_scientific_authorization": true
  }
}