Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/09/0ef6085401c408351c1882d0382bb2/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/09/0ef6085401c408351c1882d0382bb2/.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/c4/dc1828e7f965379704ea4540409db6/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.arriba.fusions.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/stage-eb5d3959-7137-45a9-9f26-41f9201dcf7f/81/be38f7f47cc30e4a107d9e602cb8fb/arriba_filter_config.yaml
==> STAGING COMPLETE (5 inputs)

  AIH curated blacklist: matched 7 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 367
  Pass (FILTER=PASS): 63 (17.2%)
  Fail (FILTER=FAIL): 304 (82.8%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 7
  All 7 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(medium<high): 87
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 46
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 35
  confidence_below_min(medium<high);total_reads_below_min(2.0<8.0): 18
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 16
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 15
  confidence_below_min(low<high): 12
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0): 10
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 10
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 9
  confidence_below_min(medium<high);total_reads_below_min(6.0<8.0): 8
  confidence_below_min(low<high);total_reads_below_min(6.0<8.0): 7
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 7
  confidence_below_min(medium<high);total_reads_below_min(7.0<8.0): 4
  total_reads_below_min(5.0<8.0): 3

Breakdown by confidence:
  high: 63 pass, 9 fail (total: 72)
  low: 0 pass, 115 fail (total: 115)
  medium: 0 pass, 180 fail (total: 180)
Arriba filter: 367 rows -> 63 PASS; wrote aih-tih-sc-8e3550-R1_A23YTGFLT4_1.arriba.fusions.filtered.tsv and aih-tih-sc-8e3550-R1_A23YTGFLT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: aih-tih-sc-8e3550-R1_A23YTGFLT4_1.arriba.fusions.filter_summary.txt