Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d7/70d1ec1b59a5ab9a0d105d00642a6c/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d7/70d1ec1b59a5ab9a0d105d00642a6c/.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/a9/0ff0b406347fad511e107d0d640d35/aih-tih-sc-2a8dd7-R1_A23WJ53LT4_1.arriba.fusions.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 9 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 187
  Pass (FILTER=PASS): 8 (4.3%)
  Fail (FILTER=FAIL): 179 (95.7%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 9
  All 9 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 23
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 21
  confidence_below_min(medium<high): 20
  confidence_below_min(low<high): 19
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 18
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 16
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 11
  confidence_below_min(medium<high);total_reads_below_min(7.0<8.0): 10
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 6
  confidence_below_min(medium<high);total_reads_below_min(2.0<8.0): 5
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 5
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 5
  confidence_below_min(medium<high);aih_curated_blacklist: 4
  confidence_below_min(low<high);total_reads_below_min(6.0<8.0): 4
  total_reads_below_min(7.0<8.0): 2

Breakdown by confidence:
  high: 8 pass, 5 fail (total: 13)
  low: 0 pass, 104 fail (total: 104)
  medium: 0 pass, 70 fail (total: 70)
Arriba filter: 187 rows -> 8 PASS; wrote aih-tih-sc-2a8dd7-R1_A23WJ53LT4_1.arriba.fusions.filtered.tsv and aih-tih-sc-2a8dd7-R1_A23WJ53LT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: aih-tih-sc-2a8dd7-R1_A23WJ53LT4_1.arriba.fusions.filter_summary.txt