Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a8/3e3d38c93420dd3d44a6990bf23e4a/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/06/f6ab786722cd8bf452e75d7bdfe560/aih-tih-sc-b7f13b-R1_A23WJ53LT4_1.arriba.fusions.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a8/3e3d38c93420dd3d44a6990bf23e4a/.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 9 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 314
  Pass (FILTER=PASS): 81 (25.8%)
  Fail (FILTER=FAIL): 233 (74.2%)

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

Failure reasons (top 15):
  confidence_below_min(medium<high): 63
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 43
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 19
  confidence_below_min(low<high): 18
  confidence_below_min(medium<high);total_reads_below_min(7.0<8.0): 15
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 11
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 9
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 9
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 7
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 7
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 7
  confidence_below_min(low<high);total_reads_below_min(7.0<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(medium<high);total_reads_below_min(5.0<8.0): 3

Breakdown by confidence:
  high: 81 pass, 5 fail (total: 86)
  low: 0 pass, 124 fail (total: 124)
  medium: 0 pass, 104 fail (total: 104)
Arriba filter: 314 rows -> 81 PASS; wrote aih-tih-sc-b7f13b-R1_A23WJ53LT4_1.arriba.fusions.filtered.tsv and aih-tih-sc-b7f13b-R1_A23WJ53LT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: aih-tih-sc-b7f13b-R1_A23WJ53LT4_1.arriba.fusions.filter_summary.txt