Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8c/1ed8f46543a3d31ab42a39b73bce90/aih-tih-sc-e4cfff-R1_A23WJ53LT4_1.arriba.fusions.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e2/83c88dabe76f05e3cde706b5548b53/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e2/83c88dabe76f05e3cde706b5548b53/.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 3 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 133
  Pass (FILTER=PASS): 13 (9.8%)
  Fail (FILTER=FAIL): 120 (90.2%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 3
  All 3 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 28
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 24
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 15
  confidence_below_min(medium<high): 12
  confidence_below_min(medium<high);total_reads_below_min(7.0<8.0): 6
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 4
  confidence_below_min(low<high);total_reads_below_min(7.0<8.0): 4
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0): 4
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 4
  confidence_below_min(medium<high);total_reads_below_min(2.0<8.0): 3
  confidence_below_min(medium<high);aih_curated_blacklist: 3
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 3
  total_reads_below_min(5.0<8.0): 2
  total_reads_below_min(3.0<8.0): 2
  confidence_below_min(low<high): 2

Breakdown by confidence:
  high: 13 pass, 6 fail (total: 19)
  low: 0 pass, 34 fail (total: 34)
  medium: 0 pass, 80 fail (total: 80)
Arriba filter: 133 rows -> 13 PASS; wrote aih-tih-sc-e4cfff-R1_A23WJ53LT4_1.arriba.fusions.filtered.tsv and aih-tih-sc-e4cfff-R1_A23WJ53LT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: aih-tih-sc-e4cfff-R1_A23WJ53LT4_1.arriba.fusions.filter_summary.txt