Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3e/daac8fdd187ccd6f777ca0d5ebcc5b/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3e/daac8fdd187ccd6f777ca0d5ebcc5b/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-resources/AIH/rna/GRCh38/blacklist_breakpoint_database_2026-04-27.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4f/b4b9835681e6b60618fd0e5e75ba6c/FFPE_V4_0001_RNA_0001_B23LG7FLT4_1.arriba.fusions.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/stage-f79a17a0-988d-46c3-a0fc-cc7f26b06d9c/2f/783d5e3fc4bb0e4fc378bb3e8b5e61/arriba_filter_config.yaml
==> STAGING COMPLETE (5 inputs)

  AIH curated blacklist: matched 8 fusion rows (breakpoint_ID in qualified set)

================================================================================
ARRIBA FILTERING SUMMARY
================================================================================

Total fusions: 125
  Pass (FILTER=PASS): 19 (15.2%)
  Fail (FILTER=FAIL): 106 (84.8%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 8
  All 8 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 16
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 12
  confidence_below_min(low<high): 12
  confidence_below_min(low<high);total_reads_below_min(7.0<8.0): 11
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 10
  confidence_below_min(medium<high): 8
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 8
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 6
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 6
  confidence_below_min(low<high);total_reads_below_min(6.0<8.0): 3
  confidence_below_min(medium<high);aih_curated_blacklist: 3
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 3
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0);aih_curated_blacklist: 2
  aih_curated_blacklist: 1
  confidence_below_min(medium<high);total_reads_below_min(7.0<8.0): 1

Breakdown by confidence:
  high: 19 pass, 1 fail (total: 20)
  low: 0 pass, 85 fail (total: 85)
  medium: 0 pass, 20 fail (total: 20)
Arriba filter: 125 rows -> 19 PASS; wrote FFPE_V4_0001_RNA_0001_B23LG7FLT4_1.arriba.fusions.filtered.tsv and FFPE_V4_0001_RNA_0001_B23LG7FLT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: FFPE_V4_0001_RNA_0001_B23LG7FLT4_1.arriba.fusions.filter_summary.txt