{ "schema": "nmd-vcell-analysis-attempt-ledger/1.1", "release": "multidisease_release_v02", "generated_at": "2026-08-05T09:03:39.361928+00:00", "policy": "Failed or transport-aborted attempts are retained and excluded from claims; only a complete run may populate the release summary. Post-run serialization and figure-layout operations must be hash-bound, table-preserving and separately audited.", "attempts": [ { "schema": "nmd-vcell-analysis-attempt/1.0", "release": "multidisease_release_v02", "attempt": 1, "status": "FAILED_PARTIAL_OUTPUTS_QUARANTINED", "stage": "FSHD post-QC/post-UMAP and post gene-level pseudobulk; before module effects, figures, SMA analysis, unified summary, and release completion", "error": "unable to find an inherited method for function 'cpm' for signature 'DGEList'", "cause": "The cpm symbol resolved to a masked S4 generic instead of edgeR::cpm after the single-cell packages were attached.", "results_used_for_claims": false, "partial_outputs": [ "FSHD sample QC", "FSHD marker-defined cluster summaries", "FSHD gene-level line-blocked pseudobulk effects", "FSHD prespecified-candidate effect subset" ], "candidate_ranking_performed": false, "remediation_scope": "Explicit edgeR and limma namespace qualification plus a dispatch self-test.", "analysis_design_changes": [], "threshold_changes": [], "candidate_rule_changes": [] }, { "schema": "nmd-vcell-analysis-attempt/1.0", "release": "multidisease_release_v02", "attempt": 2, "status": "ABORTED_TRANSPORT_SESSION", "stage": "FSHD sample-wise QC completed; merged-object integration had not emitted its UMAP checkpoint", "observed_exit": "R process and SSH-owned process tree disappeared without an R error, OOM event, core dump, or completion marker.", "results_used_for_claims": false, "new_effect_outputs_completed": false, "candidate_ranking_performed": false, "remediation_scope": "Run the identical analysis in a detached setsid/nohup job so SSH transport lifetime cannot terminate R.", "analysis_design_changes": [], "threshold_changes": [], "candidate_rule_changes": [] }, { "schema": "nmd-vcell-analysis-attempt/1.0", "release": "multidisease_release_v02", "attempt": 3, "status": "FAILED_PARTIAL_OUTPUTS_QUARANTINED", "stage": "FSHD post-QC/post-UMAP, gene-level pseudobulk, module effects, metadata export, and first figure-device initialization; before complete FSHD figure family, SMA analysis, unified summary, and release completion", "error": "ggplot2 could not find UMAP_1 while computing the first FSHD embedding layer", "cause": "The installed Seurat version emitted lower-case reduction columns (umap_1 and umap_2), while the plotting contract expected canonical upper-case UMAP_1 and UMAP_2 names.", "results_used_for_claims": false, "partial_outputs": [ "FSHD sample QC", "FSHD marker-defined cluster summaries", "FSHD gene-level line-blocked pseudobulk effects", "FSHD prespecified-candidate effect subset", "FSHD module effects and sample module scores", "FSHD cell metadata and embeddings", "incomplete FSHD PDF device output" ], "candidate_ranking_performed": false, "remediation_scope": "Canonicalize reduction-coordinate column names at the plotting/export boundary and add a dedicated self-test.", "analysis_design_changes": [], "threshold_changes": [], "candidate_rule_changes": [] }, { "schema": "nmd-vcell-analysis-attempt/1.0", "release": "multidisease_release_v02", "attempt": 4, "status": "FAILED_PARTIAL_OUTPUTS_QUARANTINED", "stage": "FSHD analysis and figure family complete; SMA sample QC, integration, marker annotation, line-level gene effects and module effects complete; before SMA composition/state effects, cell-metadata export, SMA figures, unified Figure 9, summary and release completion", "error": "SMA composition-stage merge failed because the requested biological_line key was not uniquely valid", "cause": "A generic data-frame merge was used where the design contract requires a unique biological-line-to-genotype map. The same run also exposed rank-deficient sample-batch coefficients in the visualization-only SMA PCA correction because technical libraries are nested within biological lines.", "results_used_for_claims": false, "partial_outputs": [ "complete FSHD tables and unrefined figure family", "SMA sample QC and descriptive cluster summaries", "SMA line-level directional gene and module effects", "incomplete three-row SMA candidate subset" ], "candidate_ranking_performed": false, "remediation_scope": "Replace generic SMA merges with a validated one-to-one biological-line map; replace rank-deficient nested-batch regression with within-line technical-library PC centering that preserves line centroids; add direct self-tests.", "visualization_only_changes": [ "SMA PCA geometry uses within-line technical-library centering instead of a rank-deficient sample-batch design" ], "analysis_design_changes": [], "threshold_changes": [], "candidate_rule_changes": [] }, { "schema": "nmd-vcell-analysis-attempt/1.0", "release": "multidisease_release_v02", "attempt": 5, "status": "FAILED_PARTIAL_OUTPUTS_QUARANTINED", "stage": "FSHD analysis and unrefined figure family complete; SMA sample QC, integration, marker scoring, line-level gene effects and module effects complete; before valid SMA composition/state effects, cell-metadata export, SMA figures, unified Figure 9, summary and release completion", "error": "SMA state-eligibility aggregation failed because marker_state was absent after every marker-state assignment resolved to missing", "cause": "Seurat 5 prefixed numeric AverageExpression cluster columns as g0/g1/... while seurat_clusters retained 0/1/... identifiers. The unvalidated lookup therefore assigned NA to every cell state, produced empty composition tables and failed at the first formula that required marker_state.", "formal_log_sha256": "6ffcb207aedbf858b94e5adc707e1e6d6d34e11b3d149d33214681c094f22de6", "script_snapshot_sha256": "01ff22c10a26511e4be70028b0e59fc38c47b483c5d68f46be7ffe2d6caacf76", "results_used_for_claims": false, "partial_outputs": [ "complete FSHD tables and unrefined figure family", "SMA sample QC and descriptive cluster score table", "SMA line-level directional gene and module effects", "invalid empty SMA composition tables" ], "candidate_ranking_performed": false, "remediation_scope": "Canonicalize Seurat-prefixed AverageExpression cluster IDs against object cluster IDs before marker-state lookup; hard-fail on any missing assignment or empty composition matrix; add direct self-tests.", "visualization_only_changes": [], "analysis_design_changes": [], "threshold_changes": [], "candidate_rule_changes": [] }, { "schema": "nmd-vcell-analysis-attempt/1.0", "release": "multidisease_release_v02", "attempt": 6, "status": "COMPLETE", "transport": "detached setsid/nohup job", "formal_log": "logs/formal_run_attempt6.log", "formal_log_sha256": "cc8d54cbaa1a7e7056887390ad0120a32a628e2c1e7a0a888c1c0d15df177318", "candidate_table_finalization": { "path": "candidate_table_finalization.json", "log": "logs/formal_run_attempt6_candidate_table_finalization.log", "log_sha256": "6221d8876914e5abe0c664ac3a63e904bcd4148cedb3fed12efcf449af405581", "fshd_expected_rows": 24, "fshd_filtered_rows": 16, "sma_expected_rows": 3, "sma_filtered_rows": 0 }, "figure_refinement": { "path": "figure_refinement.json", "log": "logs/formal_run_attempt6_figure_refinement.log", "log_sha256": "623a755e1d2cb01828271f671be2eceaeec4ca740733bbab270882b931a00907", "fshd_cells_plotted": 30000, "sma_cells_plotted": 30000, "statistical_tables_modified": false }, "qc_tsv_serialization_repair": { "path": "qc_tsv_serialization_repair.json", "log": "logs/formal_run_attempt6_qc_serialization_repair.log", "log_sha256": "9d0a4113ec30e2154e6cdba40831573600ab4855da971f7ed49c5f0250bdf203", "scope": "serialization only", "statistical_tables_modified": false, "files": [ { "file": "fshd_gse303359_sample_qc.tsv", "expected_columns": 20, "pre_repair_physical_data_lines": 24, "post_repair_logical_rows": 8, "continuation_lines_folded": 16, "nonfinal_fields_modified": false, "pre_repair_sha256": "c56c069bf941d2e53826245fe6c31fa27f0987f1624da27f21c5bd3ca1752253", "post_repair_sha256": "f74f9161a0c6a0b5040929b9c41cd194fe7c4c793b08346f19ea22f6e657361c", "archived_source": "results/multidisease_release_v02/logs/formal_run_attempt6_qc_serialization_pre_repair/fshd_gse303359_sample_qc.tsv.malformed" }, { "file": "sma_gse290980_sample_qc.tsv", "expected_columns": 20, "pre_repair_physical_data_lines": 24, "post_repair_logical_rows": 8, "continuation_lines_folded": 16, "nonfinal_fields_modified": false, "pre_repair_sha256": "d2426fd46d84b06ea6685825aec00fe4225673310a84e5931b37782e16c55793", "post_repair_sha256": "7781178c37fdfa7d9ed40baf449b5486d64ab150be3cfbcc15581e48d092676b", "archived_source": "results/multidisease_release_v02/logs/formal_run_attempt6_qc_serialization_pre_repair/sma_gse290980_sample_qc.tsv.malformed" } ] }, "results_used_for_claims": true, "datasets": [ "GSE290980", "GSE303359" ], "candidate_promotions": 0, "analysis_design_changes_from_lock": [], "threshold_changes_from_lock": [], "candidate_rule_changes_from_lock": [] } ] }