Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fa/7b394f4c6cd3766f4c6ccadf72f502/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fa/7b394f4c6cd3766f4c6ccadf72f502/.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/48/53f649a7c5ff21d45d7a8ecaf9cbd1/aih-tih-sc-965752-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 10 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 278
  Pass (FILTER=PASS): 30 (10.8%)
  Fail (FILTER=FAIL): 248 (89.2%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 10
  All 10 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(medium<high): 79
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 27
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 22
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 22
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 18
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 16
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 11
  confidence_below_min(low<high): 11
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0): 8
  confidence_below_min(medium<high);total_reads_below_min(2.0<8.0): 5
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 5
  confidence_below_min(medium<high);aih_curated_blacklist: 4
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 4
  total_reads_below_min(4.0<8.0): 2
  confidence_below_min(medium<high);total_reads_below_min(6.0<8.0): 2

Breakdown by confidence:
  high: 30 pass, 4 fail (total: 34)
  low: 0 pass, 111 fail (total: 111)
  medium: 0 pass, 133 fail (total: 133)
Arriba filter: 278 rows -> 30 PASS; wrote aih-tih-sc-965752-R1_A23WJ53LT4_1.arriba.fusions.filtered.tsv and aih-tih-sc-965752-R1_A23WJ53LT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: aih-tih-sc-965752-R1_A23WJ53LT4_1.arriba.fusions.filter_summary.txt