Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/37/62918b1191fa5964e4ecb54c96d18d/aih-tih-sc-835699-R1_A23WJ53LT4_1.arriba.fusions.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/88/b2732aadaba84969d7da5e64ee34e6/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/88/b2732aadaba84969d7da5e64ee34e6/.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 16 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 219
  Pass (FILTER=PASS): 13 (5.9%)
  Fail (FILTER=FAIL): 206 (94.1%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 16
  All 16 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(medium<high): 86
  confidence_below_min(low<high): 13
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 13
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0): 13
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 13
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 12
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 11
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 8
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 5
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 4
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 4
  confidence_below_min(low<high);total_reads_below_min(6.0<8.0): 3
  confidence_below_min(medium<high);aih_curated_blacklist: 3
  confidence_below_min(medium<high);total_reads_below_min(6.0<8.0): 3
  total_reads_below_min(7.0<8.0);aih_curated_blacklist: 2

Breakdown by confidence:
  high: 13 pass, 6 fail (total: 19)
  low: 0 pass, 74 fail (total: 74)
  medium: 0 pass, 126 fail (total: 126)
Arriba filter: 219 rows -> 13 PASS; wrote aih-tih-sc-835699-R1_A23WJ53LT4_1.arriba.fusions.filtered.tsv and aih-tih-sc-835699-R1_A23WJ53LT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: aih-tih-sc-835699-R1_A23WJ53LT4_1.arriba.fusions.filter_summary.txt