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"neuromuscular_virtual_cell/data/external/GSE288958/metadata/existing_reference_preflight/gse288958_existing_reference_sample_qc.tsv" ] }, { "scope_id": "adjacent_gfod2_project", "logical_root": "24.GFOD2", "root_present": true, "file_inventory_count": 1075, "dataset_anchor_file_count": 29, "text_files_read": 10, "dataset_bound_artifact_filename_hits": [], "dataset_bound_parameter_reference_content_hits": [], "dataset_anchor_examples": [ "24.GFOD2/configs/gse288958_m01b_scrublet_plan_v1.yaml", "24.GFOD2/configs/gse288958_m01b_sensitivity_plan_v1.yaml", "24.GFOD2/configs/gse288958_validation_compartment_freeze_v1.yaml", "24.GFOD2/data/manifests/GSE288958_GEO_samples_full_20260720.soft", "24.GFOD2/data/manifests/GSE288958_PRJNA1218529_RunInfo_20260720.csv", "24.GFOD2/data/manifests/gse288958_donor_metadata.tsv", "24.GFOD2/data/manifests/gse288958_object_cells.tsv", "24.GFOD2/data/manifests/gse288958_raw_matrix_manifest.tsv", "24.GFOD2/data/manifests/gse288958_raw_matrix_sha256.tsv", "24.GFOD2/mechanism_target_reboot/phase15_restrained_submission_figures/source_data/Figure_2/gse288958_edgeR_all_tested_genes.tsv", "24.GFOD2/mechanism_target_reboot/phase16_submission_revision_20260819/source_data/Figure_2/gse288958_edgeR_all_tested_genes.tsv", "24.GFOD2/mechanism_target_reboot/phase17_submission_revision_20260824/source_data/Figure_2/gse288958_edgeR_all_tested_genes.tsv", "24.GFOD2/reports/GSE288958_AMBIENT_AND_DOUBLET_INPUT_AUDIT.md", "24.GFOD2/runs/logs/gse288958_export_object_cells_20260720.log", "24.GFOD2/runs/logs/gse288958_m01b_sensitivity_20260720.log", "24.GFOD2/runs/logs/gse288958_milestone01_audit_20260720.log", "24.GFOD2/runs/logs/gse288958_raw_checksum_20260720.log", "24.GFOD2/runs/logs/gse288958_scrublet_20260720.log", "24.GFOD2/runs/logs/gse288958_scrublet_integration_20260720.log", "24.GFOD2/runs/logs/gse288958_scrublet_integration_isolated_20260720.log", "24.GFOD2/runs/logs/gse288958_scrublet_isolated_20260720.log", "24.GFOD2/runs/logs/gse288958_scrublet_isolated_recovery_20260720.log", "24.GFOD2/scripts/server/03_gse288958_milestone01_audit.R", "24.GFOD2/scripts/server/04_gse288958_m01b_sensitivity.R", "24.GFOD2/scripts/server/05_export_gse288958_object_cells.R", "24.GFOD2/scripts/server/05_gse288958_scrublet_audit.py", "24.GFOD2/scripts/server/06_gse288958_scrublet_integration.R", "24.GFOD2/scripts/server/07_checksum_gse288958_raw_inputs.R", "24.GFOD2/scripts/server/21_planb_gse288958_analysis.R" ] } ], "result": { "dataset_bound_artifact_filename_hits": 4, "dataset_bound_exact_parameter_content_hits": 0, "proxy_or_audit_parameter_reference_hit_count": 4, "author_evidence_file_count": 0, "exact_author_command_found": false, "exact_sample_sheet_found": false, "exact_read_cycle_contract_found": false, "exact_barcode_whitelist_found": false, "exact_reference_package_found": false, "exact_fastq_aggregation_manifest_found": false, "conclusion": "No dataset-bound exact author Cell Ranger command, sample sheet, read-cycle contract, barcode whitelist, reference package checksum or FASTQ aggregation manifest was found in the searched local scopes. Proxy plans, audit scripts and reports are retained as references but do not count as author evidence. This is an inventory-limited negative result, not proof that the materials do not exist elsewhere." }, "non_binding_rule": "Do not transfer read structure, whitelist, reference package or command parameters from another accession or another project into GSE288958.", "next_action": "Request the six author-confirmation items listed in the processing contract before claiming author-exact raw reprocessing; they are optional for the bounded read-only processed-reference context release." } }, { "artifact_id": "author_parameter_request", "state": "PRESENT", "candidate_names": [ "../author_parameter_request/gse288958_author_parameter_request.json", "../author_parameter_request/GSE288958_author_parameter_request.json" ], "path": "../author_parameter_request/gse288958_author_parameter_request.json", "size_bytes": 9884, "sha256": "9aea6ceca6c4cd4386f3f00deaddffdab616f8bb4725d327a879979a30a7da7a", "missing_fields": [], "notes": "File is present and checksum-addressed; opening and cross-object reconciliation remain separate gates.", "json": { "manifest_schema": "nmd-vcell-gse288958-author-parameter-request/1.0", "request_id": "GSE288958-AUTHOR-PARAMETERS-20260810", "checked_at": "2026-08-10", "dataset": { "geo_accession": "GSE288958", "bioproject": "PRJNA1218529", "sra_study": "SRP561176", "sample_scope": 11, "reported_processing": { "assay": "single-nucleus RNA-seq from flow-cytometry-isolated nuclei", "chemistry": "10x Genomics Single Cell Chromium 3' V3 / CG000183", "sequencing": "paired-end 200 bp; Illumina NovaSeq 6000", "software": "Cell Ranger v6.0.0", "reference_family": "human GRCh38/hg38 pre-mRNA transcriptome reference provided by 10x Genomics" } }, "purpose": "Close the six reproducibility gaps before staging the 11 SRA runs and reproducing raw_feature_bc_matrix plus filtered_feature_bc_matrix.", "current_evidence": [ { "logical_path": "24.GFOD2/data/manifests/GSE288958_GEO_samples_full_20260720.soft", "sha256": "11e68551807df06d83dbd6fce0fd4b092efb9c0d2cac3e67d0421ae0a0e73fbb", "records": 11 }, { "logical_path": "24.GFOD2/data/manifests/GSE288958_PRJNA1218529_RunInfo_20260720.csv", "sha256": "fbd26d2689d8e65482e9df4d12dcf88f9921c794fa8f6939025b3eb7cd7d267b", "records": 11 }, { "logical_path": "neuromuscular_virtual_cell/data/external/GSE288958/metadata/gse288958_parameter_recovery_audit.json", "status": "inventory-limited-negative", "exact_parameter_material_hits": 0 } ], "current_contract": { "logical_path": "neuromuscular_virtual_cell/data/external/GSE288958/metadata/gse288958_processing_contract.json", "status": "PARTIAL_PROCESSING_CONTRACT_AUTHOR_CONFIRMATION_REQUIRED", "source_method_evidence_present": true, "processing_contract_complete": false, "raw_reprocessing_authorized": false, "formal_qc_authorized": false, "disease_effect_test_authorized": false }, "request_items": [ { "item_id": "AP-01", "priority": "P0", "title": "Original Cell Ranger command, sample sheet and aggregation settings", "request": "Provide the exact command line, sample sheet or command export used for all 11 samples, including count/aggr/multi mode and any aggregation step.", "required_fields": [ "cellranger_version", "mode", "command_or_sample_sheet", "fastqs_argument_or_library_input", "transcriptome_argument", "chemistry_argument_or_auto_detection", "expect_cells_or_force_cells_if_set", "include_introns_if_set", "create_bam_if_set", "localcores_and_localmem_if_recorded", "aggregation_parameters_if_used" ], "acceptable_evidence": [ "original shell command or scheduler script", "original Cell Ranger sample sheet or multi config CSV", "author-confirmed plain-text reconstruction with explicit unknown fields" ], "not_sufficient": [ "SOFT processing prose alone", "default Cell Ranger command inferred by the analyst" ], "response_status": "PENDING" }, { "item_id": "AP-02", "priority": "P0", "title": "R1/i7/i5/R2 read-cycle allocation", "request": "Provide the actual sequencing cycle allocation and index orientation for the paired-end libraries.", "required_fields": [ "layout", "r1_cycles", "i7_cycles", "i5_cycles", "r2_cycles", "index_orientation", "instrument_run_or_flowcell_if_available" ], "acceptable_evidence": [ "BCL/FASTQ run sheet", "sequencer sample sheet", "author-confirmed cycle table" ], "not_sufficient": [ "paired-end 200 bp without per-read allocation", "generic 10x V3 specification" ], "response_status": "PENDING" }, { "item_id": "AP-03", "priority": "P0", "title": "10x barcode whitelist and chemistry detection", "request": "Provide the exact barcode whitelist name/version and whether Cell Ranger chemistry auto-detection was used.", "required_fields": [ "whitelist_name", "whitelist_version_or_release", "whitelist_file_or_package_path_if_available", "chemistry_auto_detected", "barcode_read_and_orientation" ], "acceptable_evidence": [ "Cell Ranger log", "reference/package manifest", "author-confirmed whitelist record" ], "not_sufficient": [ "assume the default 10x V3 whitelist", "barcode list recovered from a different accession" ], "response_status": "PENDING" }, { "item_id": "AP-04", "priority": "P0", "title": "Exact 10x GRCh38/hg38 pre-mRNA reference package", "request": "Provide the exact reference package identifier, release/version, build date and checksum used for Cell Ranger.", "required_fields": [ "package_id", "package_version_or_release_date", "assembly", "pre_mrna_or_intronic_policy", "reference_sha256", "fasta_gtf_or_package_manifest_if_available" ], "acceptable_evidence": [ "10x reference package manifest", "Cell Ranger reference directory checksum manifest", "author-confirmed package record" ], "not_sufficient": [ "GRCh38/hg38 family label without package identity", "a current 10x reference substituted for the historical package" ], "response_status": "PENDING" }, { "item_id": "AP-05", "priority": "P1", "title": "Feature-reference CSV usage", "request": "Confirm whether a Cell Ranger feature-reference CSV was supplied; if yes, provide the file and checksum, and if no, explicitly record none.", "required_fields": [ "feature_reference_used", "feature_reference_filename_if_used", "feature_reference_sha256_if_used", "feature_reference_columns_if_used", "explicit_none_confirmation_if_not_used" ], "acceptable_evidence": [ "original Cell Ranger command/config", "feature-reference CSV", "author-confirmed none/used statement" ], "not_sufficient": [ "public gene feature table treated as a feature-reference CSV", "assumption based on assay name" ], "response_status": "PENDING" }, { "item_id": "AP-06", "priority": "P0", "title": "FASTQ naming, lane/run aggregation and library IDs", "request": "Provide the mapping from the 11 GSM/sample units to SRA run IDs, library IDs, flowcell/lane information and FASTQ filename patterns.", "required_fields": [ "sample_or_gsm", "sra_run_or_original_run_id", "library_id", "flowcell_and_lane_if_available", "fastq_filename_pattern", "lane_aggregation_rule", "sample_sheet_sample_id_or_library_id" ], "acceptable_evidence": [ "FASTQ manifest", "sample sheet", "sequencing core delivery manifest", "author-confirmed mapping table" ], "not_sufficient": [ "SRA RunInfo alone", "analyst-created filename convention without author confirmation" ], "response_status": "PENDING" } ], "run_scope": [ { "sample_name": "BMD_1", "gsm": "GSM8779832", "run": "SRR32206096", "disease": "BMD" }, { "sample_name": "BMD_2", "gsm": "GSM8779833", "run": "SRR32206095", "disease": "BMD" }, { "sample_name": "BMD_3", "gsm": "GSM8779834", "run": "SRR32206094", "disease": "BMD" }, { "sample_name": "DMD1", "gsm": "GSM8779835", "run": "SRR32206093", "disease": "DMD" }, { "sample_name": "DMD2", "gsm": "GSM8779836", "run": "SRR32206092", "disease": "DMD" }, { "sample_name": "DMD_3", "gsm": "GSM8779837", "run": "SRR32206100", "disease": "DMD" }, { "sample_name": "Normal1", "gsm": "GSM8779827", "run": "SRR32206102", "disease": "control" }, { "sample_name": "Normal_2", "gsm": "GSM8779828", "run": "SRR32206101", "disease": "control" }, { "sample_name": "Normal_3", "gsm": "GSM8779829", "run": "SRR32206099", "disease": "control" }, { "sample_name": "Normal_4", "gsm": "GSM8779830", "run": "SRR32206098", "disease": "control" }, { "sample_name": "Normal_5", "gsm": "GSM8779831", "run": "SRR32206097", "disease": "control" } ], "response_format": { "preferred": "Fill gse288958_author_parameter_response.template.json or return equivalent JSON/Markdown with one response per item_id.", "required_provenance": [ "provider or author", "date", "source filename or statement", "whether exact/original or reconstructed", "checksum for every returned file" ], "unknown_field_rule": "Use UNKNOWN_AUTHOR_NOT_RECORDED when the field cannot be recovered; do not silently fill a default.", "signed_confirmation_rule": "If an original file is unavailable, the author should explicitly confirm which fields are known, reconstructed or unavailable." }, "validation_sequence": [ "Checksum every returned file and bind it to the response item.", "Rebuild gse288958_processing_contract.json with the returned values and source paths.", "Check that all P0 items are exact or author-confirmed; retain explicit unknowns.", "Only after contract completion, stage the 11 SRA runs and record per-run checksums.", "Generate raw_feature_bc_matrix and filtered_feature_bc_matrix, then reconcile sample/cell/feature identities before formal QC." ], "prohibited_substitutes": [ "Parameters from another accession or another project", "Default 10x/Cell Ranger settings not confirmed for this dataset", "Published method prose used as a substitute for exact read cycles or package checksum", "Filtered matrix, proxy annotation or Scrublet sensitivity as a substitute for raw processing provenance" ], "claim_boundary": "This package requests missing reproducibility evidence. It does not authorize SRA download, raw reprocessing, formal QC, disease-effect testing or DMD candidate transfer. Direct DMD candidate perturbation truth remains 0/21." } }, { "artifact_id": "processing_contract", "state": "PRESENT", "candidate_names": [ "../metadata/gse288958_processing_contract.json", "../metadata/GSE288958_processing_contract.json" ], "path": "../metadata/gse288958_processing_contract.json", "size_bytes": 32794, "sha256": "e90a5f3dccb2e46969e2d30f183181244d9094a06efc56ed8d67ae803f152a7f", "missing_fields": [], "notes": "File is present and checksum-addressed; opening and cross-object reconciliation remain separate gates.", "json": { "manifest_schema": "nmd-vcell-gse288958-processing-contract/1.0", "dataset_id": "GSE288958", "checked_at": "2026-09-09", "status": "PARTIAL_PROCESSING_CONTRACT_AUTHOR_CONFIRMATION_REQUIRED", "source_scope": { "geo_url": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE288958", "bioproject": "PRJNA1218529", "sra_study": "SRP561176", "sample_scope": 11, "disease_scope": { "control": 5, "bmd": 3, "dmd": 3 } }, "evidence": { "geo_sample_soft": { "path": "24.GFOD2/data/manifests/GSE288958_GEO_samples_full_20260720.soft", "sha256": "11e68551807df06d83dbd6fce0fd4b092efb9c0d2cac3e67d0421ae0a0e73fbb", "sample_records": 11 }, "sra_runinfo": { "path": "24.GFOD2/data/manifests/GSE288958_PRJNA1218529_RunInfo_20260720.csv", "sha256": "fbd26d2689d8e65482e9df4d12dcf88f9921c794fa8f6939025b3eb7cd7d267b", "run_records": 11 } }, "parameter_recovery_search": { "manifest_schema": "nmd-vcell-gse288958-parameter-recovery-audit/1.0", "dataset_id": "GSE288958", "checked_at": "2026-09-09", "audit_scope": "local workspace project plus adjacent GFOD2 project inventory", "search_policy": { "dataset_anchors": [ "GSE288958", "PRJNA1218529", "SRP561176" ], "filename_artifacts": [ "cellranger_command", "sample_sheet", "fastq_manifest", "barcode_whitelist", "read_cycle", "reference_package" ], "exact_content_artifacts": [ "cellranger_command", "sample_sheet", "read_cycle", "barcode_whitelist", "reference_package", "fastq_manifest" ], "excluded_binary_or_generated_content": [ "RDS/H5/H5AD/TAR/GZIP/ZIP/PDF/image files", "generated public/Next build directories", "this audit, processing contract and P15/P16 reports" ] }, "scopes": [ { "scope_id": "current_project", "logical_root": "neuromuscular_virtual_cell", "root_present": true, "file_inventory_count": 15366, "dataset_anchor_file_count": 107, "text_files_read": 29, "dataset_bound_artifact_filename_hits": [ { "path": "neuromuscular_virtual_cell/data/external/GSE288958/metadata/fastq_layout_preflight/SRR32206102/fasterq_output_10x_v3_whitelist_validation.json", "artifact_ids": [ "barcode_whitelist" ] }, { "path": "neuromuscular_virtual_cell/data/external/GSE288958/metadata/fastq_layout_preflight/SRR32206102/sra_spot_10x_v3_whitelist_validation.json", "artifact_ids": [ "barcode_whitelist" ] }, { "path": "neuromuscular_virtual_cell/reports/P20_GSE288958_FASTQ_LAYOUT_PREFLIGHT_20260811.md", "artifact_ids": [ "fastq_manifest" ] }, { "path": "neuromuscular_virtual_cell/reports/P22_GSE288958_CELLRANGER_SUBSET_PREFLIGHT_20260811.md", "artifact_ids": [ "cellranger_command" ] } ], "dataset_bound_parameter_reference_content_hits": [ { "path": "neuromuscular_virtual_cell/reports/P18_GSE288958_REMOTE_RAW_EXECUTION_IN_PROGRESS_20260810.md", "artifact_ids": [ "read_cycle", "barcode_whitelist", "reference_package", "fastq_manifest" ] }, { "path": "neuromuscular_virtual_cell/reports/P19_GSE288958_DOWNSTREAM_PREFLIGHT_20260811.md", "artifact_ids": [ "cellranger_command", "sample_sheet", "barcode_whitelist", "reference_package" ] }, { "path": "neuromuscular_virtual_cell/reports/P20_GSE288958_FASTQ_LAYOUT_PREFLIGHT_20260811.md", "artifact_ids": [ "sample_sheet", "read_cycle", "barcode_whitelist", "reference_package" ] }, { "path": "neuromuscular_virtual_cell/reports/P22_GSE288958_CELLRANGER_SUBSET_PREFLIGHT_20260811.md", "artifact_ids": [ "barcode_whitelist" ] } ], "dataset_anchor_examples": [ 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"neuromuscular_virtual_cell/data/external/GSE288958/metadata/existing_reference_preflight/candidate_context_overlay/gse288958_candidate_context_overlay.json", "neuromuscular_virtual_cell/data/external/GSE288958/metadata/existing_reference_preflight/candidate_context_overlay/gse288958_candidate_context_overlay.tsv", "neuromuscular_virtual_cell/data/external/GSE288958/metadata/existing_reference_preflight/candidate_context_triage/gse288958_candidate_context_triage.json", "neuromuscular_virtual_cell/data/external/GSE288958/metadata/existing_reference_preflight/candidate_context_triage/gse288958_candidate_context_triage.tsv", "neuromuscular_virtual_cell/data/external/GSE288958/metadata/existing_reference_preflight/candidate_guide_reference_coverage/gse288958_candidate_guide_reference_coverage.json", "neuromuscular_virtual_cell/data/external/GSE288958/metadata/existing_reference_preflight/candidate_guide_reference_coverage/gse288958_candidate_guide_reference_coverage.tsv", "neuromuscular_virtual_cell/data/external/GSE288958/metadata/existing_reference_preflight/candidate_validation_queue/gse288958_candidate_validation_queue.json", "neuromuscular_virtual_cell/data/external/GSE288958/metadata/existing_reference_preflight/candidate_validation_queue/gse288958_candidate_validation_queue.tsv", "neuromuscular_virtual_cell/data/external/GSE288958/metadata/existing_reference_preflight/existing_matrix_qc_audit/existing_matrix_qc_audit.json", "neuromuscular_virtual_cell/data/external/GSE288958/metadata/existing_reference_preflight/existing_matrix_qc_audit/existing_matrix_qc_audit.md", "neuromuscular_virtual_cell/data/external/GSE288958/metadata/existing_reference_preflight/existing_matrix_qc_audit/existing_matrix_qc_by_sample.tsv", "neuromuscular_virtual_cell/data/external/GSE288958/metadata/existing_reference_preflight/gse288958_celltype_counts_by_sample.tsv", "neuromuscular_virtual_cell/data/external/GSE288958/metadata/existing_reference_preflight/gse288958_existing_reference_preflight.json", "neuromuscular_virtual_cell/data/external/GSE288958/metadata/existing_reference_preflight/gse288958_existing_reference_sample_qc.tsv" ] }, { "scope_id": "adjacent_gfod2_project", "logical_root": "24.GFOD2", "root_present": true, "file_inventory_count": 1075, "dataset_anchor_file_count": 29, "text_files_read": 10, "dataset_bound_artifact_filename_hits": [], "dataset_bound_parameter_reference_content_hits": [], "dataset_anchor_examples": [ "24.GFOD2/configs/gse288958_m01b_scrublet_plan_v1.yaml", "24.GFOD2/configs/gse288958_m01b_sensitivity_plan_v1.yaml", "24.GFOD2/configs/gse288958_validation_compartment_freeze_v1.yaml", "24.GFOD2/data/manifests/GSE288958_GEO_samples_full_20260720.soft", "24.GFOD2/data/manifests/GSE288958_PRJNA1218529_RunInfo_20260720.csv", "24.GFOD2/data/manifests/gse288958_donor_metadata.tsv", "24.GFOD2/data/manifests/gse288958_object_cells.tsv", "24.GFOD2/data/manifests/gse288958_raw_matrix_manifest.tsv", "24.GFOD2/data/manifests/gse288958_raw_matrix_sha256.tsv", "24.GFOD2/mechanism_target_reboot/phase15_restrained_submission_figures/source_data/Figure_2/gse288958_edgeR_all_tested_genes.tsv", "24.GFOD2/mechanism_target_reboot/phase16_submission_revision_20260819/source_data/Figure_2/gse288958_edgeR_all_tested_genes.tsv", "24.GFOD2/mechanism_target_reboot/phase17_submission_revision_20260824/source_data/Figure_2/gse288958_edgeR_all_tested_genes.tsv", "24.GFOD2/reports/GSE288958_AMBIENT_AND_DOUBLET_INPUT_AUDIT.md", "24.GFOD2/runs/logs/gse288958_export_object_cells_20260720.log", "24.GFOD2/runs/logs/gse288958_m01b_sensitivity_20260720.log", "24.GFOD2/runs/logs/gse288958_milestone01_audit_20260720.log", "24.GFOD2/runs/logs/gse288958_raw_checksum_20260720.log", "24.GFOD2/runs/logs/gse288958_scrublet_20260720.log", "24.GFOD2/runs/logs/gse288958_scrublet_integration_20260720.log", "24.GFOD2/runs/logs/gse288958_scrublet_integration_isolated_20260720.log", "24.GFOD2/runs/logs/gse288958_scrublet_isolated_20260720.log", "24.GFOD2/runs/logs/gse288958_scrublet_isolated_recovery_20260720.log", "24.GFOD2/scripts/server/03_gse288958_milestone01_audit.R", "24.GFOD2/scripts/server/04_gse288958_m01b_sensitivity.R", "24.GFOD2/scripts/server/05_export_gse288958_object_cells.R", "24.GFOD2/scripts/server/05_gse288958_scrublet_audit.py", "24.GFOD2/scripts/server/06_gse288958_scrublet_integration.R", "24.GFOD2/scripts/server/07_checksum_gse288958_raw_inputs.R", "24.GFOD2/scripts/server/21_planb_gse288958_analysis.R" ] } ], "result": { "dataset_bound_artifact_filename_hits": 4, "dataset_bound_exact_parameter_content_hits": 0, "proxy_or_audit_parameter_reference_hit_count": 4, "author_evidence_file_count": 0, "exact_author_command_found": false, "exact_sample_sheet_found": false, "exact_read_cycle_contract_found": false, "exact_barcode_whitelist_found": false, "exact_reference_package_found": false, "exact_fastq_aggregation_manifest_found": false, "conclusion": "No dataset-bound exact author Cell Ranger command, sample sheet, read-cycle contract, barcode whitelist, reference package checksum or FASTQ aggregation manifest was found in the searched local scopes. Proxy plans, audit scripts and reports are retained as references but do not count as author evidence. This is an inventory-limited negative result, not proof that the materials do not exist elsewhere." }, "non_binding_rule": "Do not transfer read structure, whitelist, reference package or command parameters from another accession or another project into GSE288958.", "next_action": "Request the six author-confirmation items listed in the processing contract before claiming author-exact raw reprocessing; they are optional for the bounded read-only processed-reference context release." }, "author_parameter_request": { "path": "neuromuscular_virtual_cell/data/external/GSE288958/author_parameter_request/gse288958_author_parameter_request.json", "response_template": "neuromuscular_virtual_cell/data/external/GSE288958/author_parameter_request/gse288958_author_parameter_response.template.json", "status": "AUTHOR_PARAMETER_REQUEST_PACKAGE_READY_RESPONSE_PENDING" }, "execution_authorization": { "source": "explicit user authorization in current task", "status_path": "data/external/GSE288958/metadata/gse288958_execution_status.json", "raw_reprocessing_authorized": false, "formal_qc_authorized": false, "disease_effect_test_authorized": false, "execution_state": { "sra_raw_reads": { "status": "DUPLICATE_DOWNLOAD_CLEANED_EXISTING_REFERENCE_RETAINED", "tool": "NCBI SRA Toolkit 3.0.5 prefetch plus vdb-validate", "run_count": 11, "target": "sra_runs/ (removed after duplicate-download cleanup)", "download_mode": "SRA Toolkit-native sparse/range-state resume on verified /personal archive symlink; maximum two concurrent runs after /share project-quota failures; 60-second heartbeat; vdb-validate and SHA-256 gates", "supervisor_pid": null, "retry_waiter_pid": null, "retry_waiter_script": "retry_gse288958_sra_after_first_pass.sh", "retry_waiter_sha256": "cdd6bd172e172d9e1b0979a6f4d6608c65d6956a379aee26ec6f62478d2ca5f9", "completed_runs": 0, "partial_runs": 0, "quarantined_mixed_resume_runs": [ "SRR32206095", "SRR32206096" ], "quarantine_path": "/personal/virtual_cell_dmd_20260706_archives/GSE288958_20260812/quarantine_prefetch_mixed_resume_20260811/", "local_reads_present": false, "last_known_completed_runs": 7, "last_known_partial_runs": 4, "last_known_heartbeat": "2026-08-12T18:29:51+08:00", "blocker": null, "recovery_action": "User stopped and authorized cleanup of the duplicate SRA download route. The project-local native SRA directory, its symlink, stale locks and the quarantined duplicate partials were removed; the existing processed reference and all analysis artifacts were retained.", "toolkit_version": "3.0.5", "toolkit_root": "/personal/virtual_cell_dmd_20260706_archives/GSE288958_20260812/sratoolkit.3.0.5-ubuntu64", "prefetch_path": "/personal/virtual_cell_dmd_20260706_archives/GSE288958_20260812/sratoolkit.3.0.5-ubuntu64/bin/prefetch", "vdb_validate_path": "/personal/virtual_cell_dmd_20260706_archives/GSE288958_20260812/sratoolkit.3.0.5-ubuntu64/bin/vdb-validate", "fasterq_dump_path": "/personal/virtual_cell_dmd_20260706_archives/GSE288958_20260812/sratoolkit.3.0.5-ubuntu64/bin/fasterq-dump", "observed_resume_growth": "At 16:25, both active partial objects continued advancing. The 16:05:21–16:25:43 interval added approximately 30.4 MB combined (~24.9 KB/s); manifest-derived remaining partial volume is approximately 24.8 GB, giving a direct-rate estimate of about 11.5 days." }, "reference": { "status": "COMPLETE_CELLRANGER_PROXY_REFERENCE", "mode": "GRCh38 Ensembl release 113 proxy reference", "fasta": "Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz", "gtf": "Homo_sapiens.GRCh38.113.gtf.gz", "cellranger_reference_target": "cellranger_ref_GRCh38_Ensembl113_proxy_cr9", "build_policy": "gzip validation, atomic uncompressed materialization only when the Cell Ranger reference is incomplete; native genes/genes.gtf.gz is authoritative and uncompressed source material is archived after promotion", "build_result": "Cell Ranger 9 mkref completed successfully; the complete build directory was atomically promoted after all five gates passed", "author_reference_confirmed": false }, "raw_reprocessing": { "status": "NOT_REQUIRED_DUPLICATE_ROUTE_CLEANED_EXISTING_PROCESSED_REFERENCE_SUFFICIENT", "runner_pid": 53137, "runner_state": "REFERENCE_GATE_PASS; EXISTING_PROCESSED_REFERENCE_AVAILABLE; SRA_ROUTE_OPTIONAL", "planned_tool": "Cell Ranger 9.0.0 count", "planned_mode": "exploratory proxy reprocessing after SRA-to-FASTQ conversion", "sample_identity_contract": "normalized sample label plus explicit SRR/GSM mapping", "observed_sra_read_mapping": "read1=8bp technical index; read2=50bp biological Cell Ranger R1; read3=100bp biological Cell Ranger R2", "barcode_read_evidence": "SRR32206102 10,000-spot preflight: read2 first 16 bp exact 3M-february-2018_TRU whitelist match 9295/10000; read3 6/10000", "cellranger_chemistry_definition_check": "SC3Pv3-polyA uses R1[0:16] barcode, R1[16:28] UMI and R2 RNA from offset 0; 50bp R1 requires no pre-trimming", "fasterq_output_contract": "--skip-technical preserves original numbering; require _2.fastq.gz as R1 and _3.fastq.gz as R2", "per_run_fastq_gate": "10,000-record scan: fixed 50/100 bp lengths, exact paired IDs, >=0.50 R1 exact whitelist match and <=0.01 R2 match", "safe_handoff": "SRA-to-FASTQ proxy handoff is retained only for optional author-level reprocessing; it does not block existing-reference QC or context analysis", "required_output_gate": "FASTQ structure/whitelist audit, metrics, web summary, raw matrix/barcodes/features and filtered matrix/barcodes/features", "author_pipeline_reproduced": false }, "fastq_layout_preflight": { "status": "PASS_PROXY_READ_MAPPING_RECOVERED", "run": "SRR32206102", "spots_scanned": 10000, "sra_layout": "8bp technical + 50bp biological + 100bp biological", "fasterq_layout": "_2.fastq=50bp R1; _3.fastq=100bp R2", "paired_ids_match": true, "duplicate_ids": 0, "r1_exact_10x_v3_whitelist_fraction": 0.9295, "r2_exact_10x_v3_whitelist_fraction": 0.0006, "evidence_directory": "metadata/fastq_layout_preflight/SRR32206102/", "author_exact_read_contract_recovered": false }, "cellranger_subset_preflight": { "status": "PASS_STRUCTURAL_PROXY_COUNT", "run": "SRR32206102", "spots_scanned": 10000, "completed_at": "2026-08-11T23:14:57+08:00", "cellranger_version": "9.0.0", "reference": "cellranger_ref_GRCh38_Ensembl113_proxy_cr9", "r1_source": "_2.fastq.gz", "r2_source": "_3.fastq.gz", "metrics_summary": "preflight/cellranger_count_SRR32206102_10000_v2/SRR32206102_10000_cr9_preflight_v2/outs/metrics_summary.csv", "web_summary": "preflight/cellranger_count_SRR32206102_10000_v2/SRR32206102_10000_cr9_preflight_v2/outs/web_summary.html", "required_matrix_outputs": "PASS_raw_and_filtered_MEX_plus_HDF5", "structural_metrics": { "number_of_reads": 10000, "valid_barcodes": "93.8%", "valid_umis": "100.0%", "q30_barcode": "96.6%", "q30_rna": "94.9%", "q30_umi": "95.7%", "estimated_cells": 4991 }, "interpretation": "structural_only; no disease_effect_inference" }, "recovery_event": { "historical_failure_at": "2026-08-11T17:15:51+08:00", "historical_failure_stage": "reference_preparation_gate", "root_cause": "Cell Ranger 9 emitted genes/genes.gtf.gz while the preflight gate required genes/genes.gtf", "reference_build_itself": "SUCCESS", "recovery_at": "2026-08-11T22:51:58+08:00", "recovery_action": "promoted existing complete build without rebuilding STAR; removed the temporary invalid gzip-as-text alias after v1 count evidence and restarted the corrected native-gz proxy", "current_state": "RECOVERED_REFERENCE_COMPLETE_PROXY_WAITING_FOR_SRA" }, "formal_qc": { "status": "READY_EXISTING_REFERENCE_ROUTE", "runner_pid": 32314, "manifest_finalizer_pid": 32315, "runner_state": "WAITING_FOR_EXISTING_REFERENCE_QC_ROUTE; SRA_REPROCESSING_OPTIONAL", "planned_scope": "formal QC of the proxy reprocessing outputs", "input_preflight": "PASS_61189_PUBLISHED_MATRIX_CELLS_59222_PUBLISHED_OBJECT_CELLS_11_GSM", "required_packages_load_test": "PASS_DropletUtils_SingleCellExperiment_SummarizedExperiment_Matrix_scDblFinder_SoupX_scran_jsonlite", "started": false, "existing_reference_input": "formal_qc_input/existing_reference_raw_feature_bc_matrix/; 33 read-only links to the verified server-side 11-sample MEX reference", "author_formal_qc_reproduced": false }, "qc_dependencies": { "status": "COMPLETE", "bioconductor_target_version": "3.18 for R 4.3.3", "library": "formal_qc/r_lib_v2", "setup_pid_historical": 25407, "setup_process_state": "EXITED_AFTER_COMPLETE", "soupx": "PASS_1.6.2", "dropletutils": "PASS_1.22.0", "scdblfinder": "PASS_1.16.0", "completion_flag": "formal_qc/dependencies_v2.complete" }, "existing_processed_reference": { "status": "FOUND_AND_READ_ONLY_LINKED", "source_path": "LOCAL_WORKSPACE_PATH_WITHHELD/gse288958_human_muscle_reference", "link_path": "processed_reference_existing", "sample_count": 11, "matrix_count": 11, "barcode_count": 11, "feature_count": 11, "raw_archive_bytes": 359823360, "annotated_rds_bytes": 1847703081, "annotated_rds_sha256": "ff4e34c69db855640d9091cc6c1981d85b8a51fefe7c1cf40a54336bad0b4fa8", "raw_archive_sha256_remote": "782f3a18097caec58efd741253a1186598906e67c777dd3ec98066096bb86f91", "raw_archive_sha256_local_record": "fdbe0cefc3f169e112808746d8fd418927893828d40880ea325aecd3561b1931", "raw_archive_byte_identity": "NOT_ESTABLISHED_SAME_SIZE_MEMBER_AND_GZIP_VALIDATION_ONLY", "gzip_validation": "PASS", "tar_member_count": 32, "role": "existing_processed_reference_reuse; does_not_replace_author_exact_SRA_reprocessing" }, "existing_reference_preflight": { "status": "PASS_11_OF_11_SAMPLES", "report": "metadata/existing_reference_preflight/gse288958_existing_reference_preflight.json", "sample_report": "metadata/existing_reference_preflight/gse288958_existing_reference_sample_qc.tsv", "checked_at": "2026-08-12T14:20:00+08:00", "checks": [ "matrix_rows_equal_feature_rows", "matrix_cols_equal_barcode_rows", "barcode_unique", "feature_count_36601", "shared_feature_content_sha256" ], "all_sample_structural_checks_pass": true, "total_matrix_cells": 61189, "next_route": "existing_reference_qc_and_annotation_audit", "claim_boundary": "Structural reuse preflight only; not author-exact Cell Ranger reproduction, not formal ambient/doublet QC, and not direct DMD perturbation truth." }, "existing_reference_qc_risk_audit": { "status": "PASS_WITH_NORMAL_2_LOW_COMPLEXITY_FLAG", "report": "metadata/existing_reference_preflight/qc_risk_audit.md", "source_filter_summary": "metadata/existing_reference_preflight/gse288958_filter_summary_by_sample.tsv", "flagged_sample": "Normal_2", "flagged_sample_raw_cells": 4953, "flagged_sample_retained_cells": 3020, "flagged_sample_retained_percent": 62.0123203285421, "flagged_sample_median_nCount_RNA": 589, "flagged_sample_median_nFeature_RNA": 406, "other_sample_retained_percent_range": "99.662984459839-100", "next_route": "sample_aware_context_qc_with_predeclared_Normal_2_sensitivity", "claim_boundary": "QC risk flag only; no ad hoc sample deletion, no disease-effect inference, and formal ambient/doublet/final annotation gates remain unresolved." }, "existing_matrix_qc_audit": { "status": "COMPLETE_READ_ONLY_MATRIX_AUDIT", "report": "metadata/existing_reference_preflight/existing_matrix_qc_audit/existing_matrix_qc_audit.md", "sample_report": "metadata/existing_reference_preflight/existing_matrix_qc_audit/existing_matrix_qc_by_sample.tsv", "cell_report": "metadata/existing_reference_preflight/existing_matrix_qc_audit/existing_matrix_qc_by_cell.tsv.gz", "checked_at": "2026-08-12T17:10:00+08:00", "sample_count": 11, "total_raw_cells": 61189, "total_broad_gate_retained_cells": 59252, "broad_gate": "nFeature_RNA >= 300 and <= 8000; nCount_RNA >= 500; percent.mt <= 10", "flagged_sample": "Normal_2", "flagged_sample_retained_percent": 61.15485564304461, "claim_boundary": "Independent matrix-level QC audit of the existing processed reference; not author-exact Cell Ranger reproduction, not complete ambient/doublet calling, and not direct DMD perturbation truth." }, "existing_reference_formal_qc_audit": { "status": "COMPLETE_MATRIX_QC_LOW_COUNT_AMBIENT_PROFILE_MARKER_AUDIT_SOUPX_DOUBLETS_PENDING", "report": "formal_qc_input/existing_reference_qc_audit/existing_reference_formal_qc_report.json", "sample_report": "formal_qc_input/existing_reference_qc_audit/existing_reference_formal_qc_by_sample.tsv", "ambient_report": "formal_qc_input/existing_reference_qc_audit/existing_reference_ambient_estimates.tsv", "cell_report": "formal_qc_input/existing_reference_qc_audit/existing_reference_formal_cell_qc.tsv.gz", "annotation_report": "formal_qc_input/existing_reference_qc_audit/existing_reference_independent_annotation_counts.tsv", "checked_at": "2026-08-12T17:50:10+08:00", "sample_count": 11, "total_raw_cells": 61189, "total_broad_gate_retained_cells": 59237, "emptydrops_status": "UNAVAILABLE_NO_UNFILTERED_EMPTY_DROPLET_COUNTS;LOW_COUNT_AMBIENT_PROFILE_RETAINED_AS_PROXY", "soupx_status": "PENDING_TASK_LOCAL_PACKAGE_RUNTIME", "scdblfinder_status": "PENDING_TASK_LOCAL_PACKAGE_RUNTIME", "flagged_sample": "Normal_2", "claim_boundary": "Read-only existing-reference audit only. Broad gate, low-count ambient profile and independent marker scores are descriptive. This is not author-exact Cell Ranger reproduction, not complete ambient/doublet closure and not disease-effect truth." }, "existing_reference_context_sensitivity": { "status": "PASS_DESCRIPTIVE_SAMPLE_AWARE_WITH_NORMAL_2_SENSITIVITY", "report_json": "metadata/existing_reference_preflight/gse288958_sample_aware_context_sensitivity/gse288958_sample_aware_context_sensitivity.json", "report_tsv": "metadata/existing_reference_preflight/gse288958_sample_aware_context_sensitivity/gse288958_sample_aware_context_sensitivity.tsv", "checked_at": "2026-08-12T14:35:00+08:00", "statistical_unit": "sample_level_module_mean", "direction_preserved_modules": [ "FAP_fibroblast:FAP_ECM_fibrosis", "FAP_fibroblast:regeneration_stress", "macrophage_monocyte:macrophage_inflammatory_state", "myonuclei_contractile:oxidative_mito_score", "myonuclei_contractile:regeneration_stress", "satellite_myogenic:regeneration_stress" ], "direction_flip_modules": [ "macrophage_monocyte:TLR2_NOD2_sensing" ], "interpretation": "FAP/ECM fibrosis, myonuclear regeneration/stress and macrophage inflammatory context are directionally retained; macrophage TLR2/NOD2 is unstable to Normal_2 exclusion and must not be claimed as robust DMD-dominant context.", "claim_boundary": "Descriptive context sensitivity only; no p-values, disease-effect authorization, causality or direct DMD perturbation truth." } } }, "confirmed_fields": { "assay_context": "single-nucleus RNA-seq from flow-cytometry-isolated nuclei", "library_chemistry": { "platform": "10x Genomics Single Cell Chromium 3'", "version": "V3", "protocol_id": "CG000183" }, "sequencing": { "layout": "PAIRED", "reported_read_specification": "paired-end 200 bp reads", "platform": "ILLUMINA", "instrument_model": "Illumina NovaSeq 6000", "exact_read_cycle_allocation": null }, "published_processing": { "software": "Cell Ranger", "version": "6.0.0", "reference_as_reported": "human GRCh38/hg38 pre-mRNA genome transcriptome references provided by 10x Genomics", "assembly": "GRCh38/hg38", "output_format_as_reported": [ "tsv", "mtx" ] } }, "author_confirmation_required": { "exact_read_cycle_allocation": "Need R1/i7/i5/R2 cycle counts or the original Cell Ranger sample sheet; the SOFT reports paired-end 200 bp but does not expose cycle allocation.", "barcode_whitelist": "Need the exact 10x whitelist/version used by the original Cell Ranger run, including whether chemistry-specific auto-detection was used.", "reference_package": "Need the exact 10x reference package identifier, release date/version and checksum; the SOFT identifies GRCh38/hg38 pre-mRNA but not a package checksum.", "feature_reference": "Need confirmation whether any feature-reference CSV was used; the public supplement is a gene feature table, not proof of a Cell Ranger feature-reference input.", "command_and_parameters": "Need the original Cell Ranger command/sample sheet and any intronic, chemistry, cell-calling or aggregation parameters.", "fastq_manifest": "Need confirmation of FASTQ naming, lane/run aggregation and per-sample library IDs before reprocessing." }, "gates": { "source_method_evidence_present": true, "chemistry_identified": true, "reference_family_identified": true, "published_cellranger_version_identified": true, "exact_read_cycle_allocation_confirmed": false, "barcode_whitelist_confirmed": false, "reference_package_checksum_confirmed": false, "original_command_confirmed": false, "processing_contract_complete": false, "raw_reprocessing_authorized": false, "formal_qc_authorized": false, "disease_effect_test_authorized": false }, "next_action": "Use the published Cell Ranger 6.0.0 and GRCh38/hg38 pre-mRNA statements as official processing context. Bind the six exact author artifacts only before claiming author-exact reprocessing; they are optional for bounded read-only reference use.", "claim_boundary": "The contract records the official published processing recipe and separates it from unresolved author-exact execution artifacts. The existing-reference audit may support bounded read-only context, while author-exact reproduction, author QC and DMD candidate perturbation truth remain unclaimed." } }, { "artifact_id": "raw_cell_inventory", "state": "PRESENT", "candidate_names": [ "raw_cell_inventory.csv", "gse288958_raw_cell_inventory.csv", "cell_inventory.csv" ], "path": "raw_cell_inventory.csv", "size_bytes": 12899748, "sha256": "98e63692a9bf08dbdcb6d5ef521108dfe4f99500da55ee4b5752cae7e735143f", "missing_fields": [], "notes": "File is present and checksum-addressed; opening and cross-object reconciliation remain separate gates.", "headers": [ "sample_id", "barcode", "cell_id", "donor_id", "disease", "biopsy_site", "age", "batch", "donor_id_status", "cell_type", "annotation_source", "annotation_status", "sample_cell_index" ] }, { "artifact_id": "feature_table", "state": "MISSING", "candidate_names": [ "features.tsv.gz", "features.tsv", "genes.tsv.gz", "genes.tsv" ], "path": null, "size_bytes": null, "sha256": null, "missing_fields": [], "notes": "Required portable-import object is not present in the candidate directory." }, { "artifact_id": "barcode_table", "state": "MISSING", "candidate_names": [ "barcodes.tsv.gz", "barcodes.tsv", "cell_barcodes.tsv" ], "path": null, "size_bytes": null, "sha256": null, "missing_fields": [], "notes": "Required portable-import object is not present in the candidate directory." }, { "artifact_id": "provenance_manifest", "state": "PRESENT", "candidate_names": [ "provenance.json", "import_manifest.json" ], "path": "import_manifest.json", "size_bytes": 4313, "sha256": "bc72c7e660c004738116b7f9542b984a9b08d0bfc13e3f60c2d7ac4b2dfa8687", "missing_fields": [], "notes": "File is present and checksum-addressed; opening and cross-object reconciliation remain separate gates.", "json": { "manifest_schema": "nmd-vcell-gse288958-multisample-source-package/1.0", "dataset_id": "GSE288958", "accession": "GSE288958", "package_type": "MULTI_SAMPLE_10X_MTX_TSV_SOURCE_PACKAGE", "source_archive": { "path": "../raw/GSE288958_RAW.tar", "size_bytes": 359823360, "sha256": "fdbe0cefc3f169e112808746d8fd418927893828d40880ea325aecd3561b1931", "tar_member_count": 32, "gzip_streams_passed": 32 }, "feature_supplement": { "path": "../raw/GSE288958_BMD_1_features.tsv.gz", "size_bytes": 333437, "sha256": "f99a146106e8e37a1bf5933e9ee3bc84139ffee889540ea0425fd3f9fbeef4a7", "gzip_validation": "PASS" }, "sample_metadata": { "path": "sample_metadata.csv", "source": "../metadata/GSE288958_family_soft_sample_metadata.csv", "rows": 11, "donor_id_state": "SAMPLE_ACCESSION_PROXY_NOT_SUBJECT_IDENTIFIER", "batch_state": "NOT_REPORTED_IN_FAMILY_SOFT" }, "sample_units": [ { "sample_id": "GSM8779827", "disease": "control", "matrix_member": "GSM8779827_Normal_1_matrix.mtx.gz", "barcode_member": "GSM8779827_Normal_1_barcodes.tsv.gz", "feature_member": "GSM8779827_Normal_1_features.tsv.gz" }, { "sample_id": "GSM8779828", "disease": "control", "matrix_member": "GSM8779828_Normal_2_matrix.mtx.gz", "barcode_member": "GSM8779828_Normal_2_barcodes.tsv.gz", "feature_member": "GSM8779828_Normal_2_features.tsv.gz" }, { "sample_id": "GSM8779829", "disease": "control", "matrix_member": "GSM8779829_Normal_3_matrix.mtx.gz", "barcode_member": "GSM8779829_Normal_3_barcodes.tsv.gz", "feature_member": "GSM8779829_Normal_3_features.tsv.gz" }, { "sample_id": "GSM8779830", "disease": "control", "matrix_member": "GSM8779830_Normal_4_matrix.mtx.gz", "barcode_member": "GSM8779830_Normal_4_barcodes.tsv.gz", "feature_member": "GSM8779830_Normal_4_features.tsv.gz" }, { "sample_id": "GSM8779831", "disease": "control", "matrix_member": "GSM8779831_Normal_5_matrix.mtx.gz", "barcode_member": "GSM8779831_Normal_5_barcodes.tsv.gz", "feature_member": "GSM8779831_Normal_5_features.tsv.gz" }, { "sample_id": "GSM8779832", "disease": "BMD", "matrix_member": "GSM8779832_BMD_1_matrix.mtx.gz", "barcode_member": "GSM8779832_BMD_1_barcodes.tsv.gz", "feature_member": "../raw/GSE288958_BMD_1_features.tsv.gz" }, { "sample_id": "GSM8779833", "disease": "BMD", "matrix_member": "GSM8779833_BMD_2_matrix.mtx.gz", "barcode_member": "GSM8779833_BMD_2_barcodes.tsv.gz", "feature_member": "GSM8779833_BMD_2_features.tsv.gz" }, { "sample_id": "GSM8779834", "disease": "BMD", "matrix_member": "GSM8779834_BMD_3_matrix.mtx.gz", "barcode_member": "GSM8779834_BMD_3_barcodes.tsv.gz", "feature_member": "GSM8779834_BMD_3_features.tsv.gz" }, { "sample_id": "GSM8779835", "disease": "DMD", "matrix_member": "GSM8779835_DMD_1_matrix.mtx.gz", "barcode_member": "GSM8779835_DMD_1_barcodes.tsv.gz", "feature_member": "GSM8779835_DMD_1_features.tsv.gz" }, { "sample_id": "GSM8779836", "disease": "DMD", "matrix_member": "GSM8779836_DMD_2_matrix.mtx.gz", "barcode_member": "GSM8779836_DMD_2_barcodes.tsv.gz", "feature_member": "GSM8779836_DMD_2_features.tsv.gz" }, { "sample_id": "GSM8779837", "disease": "DMD", "matrix_member": "GSM8779837_DMD_3_matrix.mtx.gz", "barcode_member": "GSM8779837_DMD_3_barcodes.tsv.gz", "feature_member": "GSM8779837_DMD_3_features.tsv.gz" } ], "annotation_state": "CANDIDATE_COARSE_CELLTYPE_EXPORT_PARTIAL_SENSITIVITY_AUDIT_NOT_FINAL", "annotation_object": { "path": "cell_annotations.csv", "provenance_path": "candidate_annotation_provenance.json", "object_path": "../objects/gse288958_reference_qc_umap_annotated.rds", "object_open_audit_path": "object_open_audit.json", "partial_annotation_audit_path": "annotation_audit.json", "rows": 59222, "source_object_sha256": "ff4e34c69db855640d9091cc6c1981d85b8a51fefe7c1cf40a54336bad0b4fa8", "source_object_local_state": "LOCAL_RDS_PRESENT_SHA256_VERIFIED_AND_OPENED", "annotation_level": "coarse_celltype", "annotation_audit_state": "PARTIAL_ANNOTATION_SENSITIVITY_AUDIT_FORMAL_DOUBLET_AMBIENT_UNRESOLVED" }, "provenance_state": "SOURCE_ARCHIVE_AND_GEO_SOFT_CHECKSUMMED", "object_open_state": "LOCAL_RDS_OPENED_CELL_SAMPLE_METADATA_AND_FEATURE_IDENTIFIERS_RECONCILED", "analysis_authorization": "BLOCKED_UNTIL_FORMAL_DOUBLET_AMBIENT_FINAL_ANNOTATION_AND_PROVENANCE_REVIEW", "direct_dmd_candidate_perturbation_truth": "0/21" } } ], "gates": { "source_object_present": true, "source_package_manifest_present": true, "workspace_local_path": true, "sample_metadata_schema": true, "raw_cell_inventory_present": true, "raw_cell_inventory_schema": true, "cell_annotation_schema": true, "annotation_provenance_present": true, "candidate_annotation_ids_reconciled": true, "feature_barcode_objects": true, "provenance_manifest_present": true, "source_object_opened": true, "identifiers_reconciled": true, "partial_annotation_audit": true, "formal_qc_input_request_present": true, "formal_qc_input_manifest_present": false, "formal_qc_input_preflight_present": true, "sra_recovery_manifest_present": true, "parameter_recovery_audit_present": true, "author_parameter_request_present": true, "processing_contract_present": true, "annotation_audited": true, "independent_doublet_audit": true, "independent_annotation_audit": true, "formal_ambient_audit": false, "disease_effect_test_authorized": false, "direct_dmd_candidate_perturbation_truth": false }, "pilot_reference": { "cells": 59222, "samples": 11, "selected_compartment": "endothelial", "selection_uses_disease_labels": false, "verdict": "PASS_FOR_VALIDATION_PILOT", "scope": "Validation pilot only; not the independent primary discovery cohort." }, "next_action": "Run the bounded read-only sample-aware context route with Normal_2, Scrublet and annotation-disagreement sensitivities. Ambient RNA and author-exact reprocessing remain separate optional enhancement gates.", "claim_boundary": "Object opening, identifier reconciliation, donor-wise doublet sensitivity and independent marker-label disagreement audits support bounded read-only sample-aware context. Ambient RNA remains unresolved, author-exact reprocessing remains unclaimed, and disease-effect, causality, therapeutic and direct DMD perturbation claims stay locked.", "direct_dmd_candidate_perturbation_truth": "0/21" }