Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/cf/2f04d15d7b87f56964be1daab098c5/aih-tih-sc-560d56-R1_A23WJ53LT4_1.arriba.fusions.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6c/c07f7c297ca37767bec689c50b706a/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6c/c07f7c297ca37767bec689c50b706a/.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/stage-5ae5f7b1-ce8a-4a12-9374-820c751df9c5/09/a7ecdb27117590dd6e7bf9e221420e/arriba_filter_config.yaml
==> STAGING COMPLETE (5 inputs)

  AIH curated blacklist: matched 4 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 71
  Pass (FILTER=PASS): 6 (8.5%)
  Fail (FILTER=FAIL): 65 (91.5%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 4
  All 4 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 16
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0): 10
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 7
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 6
  confidence_below_min(medium<high): 4
  confidence_below_min(medium<high);aih_curated_blacklist: 4
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 3
  confidence_below_min(medium<high);total_reads_below_min(2.0<8.0): 3
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 2
  total_reads_below_min(4.0<8.0): 2
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 2
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 2
  total_reads_below_min(7.0<8.0): 1
  total_reads_below_min(5.0<8.0): 1
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 1

Breakdown by confidence:
  high: 6 pass, 4 fail (total: 10)
  low: 0 pass, 23 fail (total: 23)
  medium: 0 pass, 38 fail (total: 38)
Arriba filter: 71 rows -> 6 PASS; wrote aih-tih-sc-560d56-R1_A23WJ53LT4_1.arriba.fusions.filtered.tsv and aih-tih-sc-560d56-R1_A23WJ53LT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: aih-tih-sc-560d56-R1_A23WJ53LT4_1.arriba.fusions.filter_summary.txt