data: record mixture and Gate D provenance

provenance/files.jsonl

@@ -10,3 +10,13 @@
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 {"schema_version": "otter.provenance.file/v1", "dataset_revision": "r4", "dataset_path": "xenofilx/gate-c/bs-pdx-graft-hg38/input.bam", "file_role": "fixture", "file_format": "BAM", "owner": {"repository": "xenofilx", "workflow": "xenofilx-gate-c", "gate": "C", "assay": "BS-PDX"}, "derivation": {"sra_accession": "SRR36187610", "paracloud_source_path": "/public3/home/scg9946/otter-gate6/toolchain-comparison-20260815T070000Z/projects/bs-pdx-SRR36187610/runs/run-20260823T034624Z-ndcwfa/work/bsmap/SRR36187610_hg38.bam", "method": "bsmap_bismark_alignment", "random_seed": null}, "counts": {"unit": "records", "input": null, "output": 90320060}, "source_commit": "79581c16f0a4b06e713bdac510e9feda17545e05", "size_bytes": 3125450579, "sha256": "ecaf4a19359074fafafd20f0baa5f994092d3af36437e538a726febfa4be61e6", "created_at_utc": "2026-08-23T03:46:24Z", "notes": "Full real BS-PDX graft hg38 BAM alignment fixture used in Gate C NM and CT/GA controls."}
 {"schema_version": "otter.provenance.file/v1", "dataset_revision": "r4", "dataset_path": "xenofilx/gate-c/bs-pdx-graft-hg38/input.bam.bai", "file_role": "fixture", "file_format": "BAI", "owner": {"repository": "xenofilx", "workflow": "xenofilx-gate-c", "gate": "C", "assay": "BS-PDX"}, "derivation": {"sra_accession": "SRR36187610", "paracloud_source_path": "/public3/home/scg9946/otter-gate6/toolchain-comparison-20260815T070000Z/projects/bs-pdx-SRR36187610/runs/run-20260823T034624Z-ndcwfa/work/bsmap/SRR36187610_hg38.bam.bai", "method": "generated_from_coordinate_sorted_bam", "random_seed": null}, "counts": {"unit": "files", "input": 1, "output": 1}, "source_commit": "79581c16f0a4b06e713bdac510e9feda17545e05", "size_bytes": 3759400, "sha256": "54acd4f37ca193e4295e2ba66eaf9814ede6201598fa0fa198dae0d6da5402d3", "created_at_utc": "2026-08-23T03:46:24Z", "notes": "Published BAI index for the full BS-PDX graft hg38 BAM alignment fixture."}
+{"schema_version": "otter.provenance.file/v1", "dataset_revision": "r5", "dataset_path": "xenofilx/mixture/rna-pdx/human0.5-replicate1/graft.bam", "file_role": "fixture", "file_format": "BAM", "owner": {"repository": "xenofilx", "workflow": "xenofilx-mixture-parity", "gate": "mixture", "assay": "RNA-PDX"}, "derivation": {"sra_accession": "SRR1039508", "paracloud_source_path": "/public3/home/scg9946/otter-gate6/evidence/gate6-human-mouse-rna-mixtures-20260903/analysis-41929279/mixture_human.bam", "method": "star_alignment_of_50_50_human_mouse_synthetic_mixture", "random_seed": null}, "counts": {"unit": "records", "input": null, "output": 1302204}, "source_commit": "79581c16f0a4b06e713bdac510e9feda17545e05", "size_bytes": 89523416, "sha256": "c4595708e48b767eaacb676a5f720e0da58a16f4d74a663962c8823a5bbaa0c5", "created_at_utc": "2026-09-03T16:35:19Z", "notes": "Human-graft STAR alignment of a 50:50 RNA-seq mixture (human SRR1039508 + mouse SRR037954; 1,000,000 truth fragments)."}
+{"schema_version": "otter.provenance.file/v1", "dataset_revision": "r5", "dataset_path": "xenofilx/mixture/rna-pdx/human0.5-replicate1/host.bam", "file_role": "fixture", "file_format": "BAM", "owner": {"repository": "xenofilx", "workflow": "xenofilx-mixture-parity", "gate": "mixture", "assay": "RNA-PDX"}, "derivation": {"sra_accession": "SRR037954", "paracloud_source_path": "/public3/home/scg9946/otter-gate6/evidence/gate6-human-mouse-rna-mixtures-20260903/analysis-41929279/mixture_mouse.bam", "method": "star_alignment_of_50_50_human_mouse_synthetic_mixture", "random_seed": null}, "counts": {"unit": "records", "input": null, "output": 1127034}, "source_commit": "79581c16f0a4b06e713bdac510e9feda17545e05", "size_bytes": 99967346, "sha256": "b7f81931f5ca47a98765a7e3f032c438217488b949d7c147cc68ab6dc4584e38", "created_at_utc": "2026-09-03T16:35:19Z", "notes": "Mouse-host STAR alignment of the same 50:50 RNA-seq mixture."}
+{"schema_version": "otter.provenance.file/v1", "dataset_revision": "r5", "dataset_path": "xenofilx/mixture/rna-pdx/human0.5-replicate1/truth.tsv", "file_role": "expected_output", "file_format": "TSV", "owner": {"repository": "xenofilx", "workflow": "xenofilx-mixture-parity", "gate": "mixture", "assay": "RNA-PDX"}, "derivation": {"sra_accession": "SRR1039508", "paracloud_source_path": "/public3/home/scg9946/otter-gate6/evidence/gate6-human-mouse-rna-mixtures-20260903/human0.5-replicate1-n1000000-pilot/truth.tsv", "method": "construction_truth_manifest", "random_seed": null}, "counts": {"unit": "templates", "input": null, "output": 1000000}, "source_commit": "79581c16f0a4b06e713bdac510e9feda17545e05", "size_bytes": 58032760, "sha256": "418673a664ed13207b3f7e3ef068283bc8c9a36764630dcb22649dcffdcbe503", "created_at_utc": "2026-09-03T14:37:00Z", "notes": "Per-fragment construction truth (fragment_id, known_source) for the 50:50 RNA mixture."}
+{"schema_version": "otter.provenance.file/v1", "dataset_revision": "r5", "dataset_path": "xenofilx/mixture/bs-pdx/human0.5-replicate1/graft.bam", "file_role": "fixture", "file_format": "BAM", "owner": {"repository": "xenofilx", "workflow": "xenofilx-mixture-parity", "gate": "mixture", "assay": "BS-PDX"}, "derivation": {"sra_accession": "SRR31480456", "paracloud_source_path": "/public3/home/scg9946/otter-gate6/evidence/gate6-human-mouse-mixtures-20260830/analysis-41761966/mixture_hg38.bam", "method": "bismark_rust_3_1_0_alignment_of_human_mouse_rrbs_mixture", "random_seed": null}, "counts": {"unit": "records", "input": null, "output": null}, "source_commit": "79581c16f0a4b06e713bdac510e9feda17545e05", "size_bytes": 70586058, "sha256": "f4ebeae5de5b07d079f72a7039ef6a2ff2e07b55a0d82e460bd21c9b58527a2e", "created_at_utc": "2026-08-30T20:15:00Z", "notes": "Human-graft Bismark Rust 3.1.0 alignment of a human/mouse RRBS mixture with XG-tagged strands."}
+{"schema_version": "otter.provenance.file/v1", "dataset_revision": "r5", "dataset_path": "xenofilx/mixture/bs-pdx/human0.5-replicate1/host.bam", "file_role": "fixture", "file_format": "BAM", "owner": {"repository": "xenofilx", "workflow": "xenofilx-mixture-parity", "gate": "mixture", "assay": "BS-PDX"}, "derivation": {"sra_accession": "SRR10025242", "paracloud_source_path": "/public3/home/scg9946/otter-gate6/evidence/gate6-human-mouse-mixtures-20260830/analysis-41761966/mixture_mm10.bam", "method": "bismark_rust_3_1_0_alignment_of_human_mouse_rrbs_mixture", "random_seed": null}, "counts": {"unit": "records", "input": null, "output": null}, "source_commit": "79581c16f0a4b06e713bdac510e9feda17545e05", "size_bytes": 20906499, "sha256": "d743ec48724a391822695ebfb9004ffa725b8c807d56a9c58f58058b280b00c3", "created_at_utc": "2026-08-30T20:17:00Z", "notes": "Mouse-host Bismark Rust 3.1.0 alignment of the same human/mouse RRBS mixture."}
+{"schema_version": "otter.provenance.file/v1", "dataset_revision": "r5", "dataset_path": "xenofilx/mixture/bs-pdx/human0.5-replicate1/truth.tsv", "file_role": "expected_output", "file_format": "TSV", "owner": {"repository": "xenofilx", "workflow": "xenofilx-mixture-parity", "gate": "mixture", "assay": "BS-PDX"}, "derivation": {"sra_accession": "SRR31480456", "paracloud_source_path": "/public3/home/scg9946/otter-gate6/evidence/gate6-human-mouse-mixtures-20260830/human0.5-replicate1-n1000000/truth.tsv", "method": "construction_truth_manifest", "random_seed": null}, "counts": {"unit": "templates", "input": null, "output": 1000000}, "source_commit": "79581c16f0a4b06e713bdac510e9feda17545e05", "size_bytes": 60684836, "sha256": "4f5d8f7abeff9247f170c48a89ce3fe9f7e3685d0b84e1d6ea05363a071fbff2", "created_at_utc": "2026-08-30T12:19:57Z", "notes": "Per-fragment construction truth for the human/mouse RRBS mixture."}
+{"schema_version": "otter.provenance.file/v1", "dataset_revision": "r5", "dataset_path": "xenofilx/gate-d/bs-pdx-srr36187610/modern_filtered.bam", "file_role": "expected_output", "file_format": "BAM", "owner": {"repository": "xenofilx", "workflow": "xenofilx-gate-d", "gate": "D", "assay": "BS-PDX"}, "derivation": {"sra_accession": "SRR36187610", "paracloud_source_path": "/public3/home/scg9946/otter-gate6/evidence/gate6-bam-nm-parity-20260826-bs-pdx/modern-xenofilx-fixed-strand-aware-41967064/output/SRR36187610_fixed_hg38_Filtered.bam", "method": "xenofilx_strand_aware_graft_selection", "random_seed": null}, "counts": {"unit": "records", "input": null, "output": 90241846}, "source_commit": "79581c16f0a4b06e713bdac510e9feda17545e05", "size_bytes": 3389005507, "sha256": "3e2c4b4c17c002be5f2a55e421bfc6364a5942a9a6c0b9165dd5a19709b05790", "created_at_utc": "2026-09-04T13:23:00Z", "notes": "Modern Xenofilx graft selection for the accepted Gate D accounting (job 41967064)."}
+{"schema_version": "otter.provenance.file/v1", "dataset_revision": "r5", "dataset_path": "xenofilx/gate-d/bs-pdx-srr36187610/legacy_filtered.bam", "file_role": "expected_output", "file_format": "BAM", "owner": {"repository": "xenofilx", "workflow": "xenofilx-gate-d", "gate": "D", "assay": "BS-PDX"}, "derivation": {"sra_accession": "SRR36187610", "paracloud_source_path": "/public3/home/scg9946/otter-gate6/evidence/gate6-bam-nm-parity-20260826-bs-pdx/legacy-picard-strand-aware-xenofilter-41967065/xenofilter-destination/Filtered_bams/SRR36187610_hg38.picard-strand-aware-nm_Filtered.bam", "method": "picard_conventional_nm_then_xenofilter", "random_seed": null}, "counts": {"unit": "records", "input": null, "output": 88011370}, "source_commit": "79581c16f0a4b06e713bdac510e9feda17545e05", "size_bytes": 3300570994, "sha256": "baac3b9b6555933cc36ada95f2bf13492fa9deb22491685aa6d23082dc866220", "created_at_utc": "2026-09-04T12:52:00Z", "notes": "Legacy Picard + XenofilteR graft selection for the accepted Gate D accounting (job 41967065)."}
+{"schema_version": "otter.provenance.file/v1", "dataset_revision": "r5", "dataset_path": "xenofilx/gate-d/bs-pdx-srr36187610/disagreements.tsv.gz", "file_role": "metric", "file_format": "TSV.GZ", "owner": {"repository": "xenofilx", "workflow": "xenofilx-gate-d", "gate": "D", "assay": "BS-PDX"}, "derivation": {"sra_accession": "SRR36187610", "paracloud_source_path": "/public3/home/scg9946/otter-gate6/evidence/gate6-bam-nm-parity-20260826-bs-pdx/fragment-membership-provenance-rerun-41967198/disagreements.tsv.gz", "method": "fragment_membership_disagreement_extract", "random_seed": null}, "counts": {"unit": "files", "input": null, "output": null}, "source_commit": "79581c16f0a4b06e713bdac510e9feda17545e05", "size_bytes": 9948100, "sha256": "6b92f0750728f660219a629316c0a729385c58567924265376c82c7e98c852b9", "created_at_utc": "2026-09-04T13:41:00Z", "notes": "Fragment-level disagreement table from the accepted Gate D membership comparison (job 41967198)."}
+{"schema_version": "otter.provenance.file/v1", "dataset_revision": "r5", "dataset_path": "xenofilx/gate-d/bs-pdx-srr36187610/score-decision-comparison.json", "file_role": "metric", "file_format": "JSON", "owner": {"repository": "xenofilx", "workflow": "xenofilx-gate-d", "gate": "D", "assay": "BS-PDX"}, "derivation": {"sra_accession": "SRR36187610", "paracloud_source_path": "/public3/home/scg9946/otter-gate6/evidence/gate6-bam-nm-parity-20260826-bs-pdx/fragment-score-decision-41973925/score-decision-comparison.json", "method": "fragment_score_decision_accounting", "random_seed": null}, "counts": {"unit": "files", "input": null, "output": null}, "source_commit": "79581c16f0a4b06e713bdac510e9feda17545e05", "size_bytes": 294391, "sha256": "b8df1375cfa6f457513d2cde3cea2cd710bbc9c50cc454faa8d37802ddf57e8f", "created_at_utc": "2026-09-04T14:34:45Z", "notes": "Score-decision accounting partitioning all 1,115,239 modern-only disagreements with zero unexplained (job 41973925)."}