Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5b/3cb1970b1e8efe5ba2614d2db70178/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/50/29b8d65f6ea3b0c322505bce0edb10/selected_gene_list.txt
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/da/a28eacc8f6f8196a0120bd59777b67/exon_skipping_catalog_labels.txt
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/48/1647375fc4ea979c9c347eef102bd3/test_harmonized_calls.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a6/348137e81738c4ba8828bf8a2a7405/patient_id_list.txt
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b7/82229be1d3f213452a481246c25dbe/alt_truth_harmonized_calls.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/stage-1878a8d8-916b-4b35-b1fa-7f540a23a9eb/1f/bfc321a3fbfe8fd37cdcb4c9ae90d5/NO_FILE
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5b/3cb1970b1e8efe5ba2614d2db70178/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/34/269842f7100ea88213b668c553ad97/truth_harmonized_calls.tsv
==> STAGING COMPLETE (9 inputs)

WARNING: ignoring unrecognized filter: E
WARNING: ignoring unrecognized filter: E
WARNING: ignoring unrecognized filter: 8
WARNING: ignoring unrecognized filter: 8
=== Fusion mode ===
Loading test...
  244540 rows
Loading truth...
  214 rows
  Test after filters: 20800 rows
  Truth after filters: 214 rows
  Arriba after per-caller filters: 445 rows
  STAR-Fusion after per-caller filters: 56 rows
  Test after per-caller filters: 501 rows
  Patient IDs in list: 76
  In test: 40, in truth: 6, both: 6
  NPA catalog:
    definition: filtered primary truth FUSION_ID_norm union filtered test FUSION_ID_norm
    |M| unique fusion events: 5
    primary truth IDs=5, test IDs=83, overlap=4, truth-only=1, test-only=79
    patient-fusion matrix cells: 76 x 5 = 380
    alternative confirmation IDs=0 (not added to M; used only for adjudicated NPA reference)
  NPA counts: primary neg_agree=373, neg_denom=374, npa_fp=1; adjudicated neg_agree=373, neg_denom=374, npa_fp=1
  Wrote fusion_adjudication_status.tsv (6 main + 93 fp_audit rows; fp original=93, adjudicated FP=93, TP_rescued=0)
  Wrote fusion_adjudication_summary.tsv
  Wrote fusion_adjudication_summary_long.tsv
  Wrote fusion_adjudication_report.txt
  Wrote fusion_adjudication_20260606_215950.log