Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a4/65a52d752447cccf144ca8851f8f69/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a4/65a52d752447cccf144ca8851f8f69/.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/23/50f585d5e65055a961646bfef2217f/aih-tih-sc-87d1a3-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 8 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 491
  Pass (FILTER=PASS): 109 (22.2%)
  Fail (FILTER=FAIL): 382 (77.8%)

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): 104
  confidence_below_min(medium<high): 64
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 37
  confidence_below_min(low<high): 23
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 21
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 21
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 15
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 14
  confidence_below_min(medium<high);total_reads_below_min(7.0<8.0): 11
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0): 11
  confidence_below_min(low<high);total_reads_below_min(6.0<8.0): 11
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 9
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 8
  confidence_below_min(medium<high);total_reads_below_min(2.0<8.0): 7
  confidence_below_min(medium<high);total_reads_below_min(6.0<8.0): 7

Breakdown by confidence:
  high: 109 pass, 9 fail (total: 118)
  low: 0 pass, 211 fail (total: 211)
  medium: 0 pass, 162 fail (total: 162)
Arriba filter: 491 rows -> 109 PASS; wrote aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.arriba.fusions.filtered.tsv and aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: aih-tih-sc-87d1a3-R1_A23WJ53LT4_1.arriba.fusions.filter_summary.txt