Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c2/0990723e2f1a25f281f85daf43bcaa/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c2/0990723e2f1a25f281f85daf43bcaa/.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/64/25253987bf2580bc4750b2d654eda6/aih-tih-sc-1274d4-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 11 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 292
  Pass (FILTER=PASS): 32 (11.0%)
  Fail (FILTER=FAIL): 260 (89.0%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 11
  All 11 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(medium<high): 90
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 39
  confidence_below_min(low<high): 22
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 20
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 16
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0): 16
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 11
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 9
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 5
  confidence_below_min(medium<high);aih_curated_blacklist: 5
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 5
  confidence_below_min(medium<high);total_reads_below_min(7.0<8.0): 3
  total_reads_below_min(4.0<8.0): 2
  total_reads_below_min(3.0<8.0): 2
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 2

Breakdown by confidence:
  high: 32 pass, 7 fail (total: 39)
  low: 0 pass, 113 fail (total: 113)
  medium: 0 pass, 140 fail (total: 140)
Arriba filter: 292 rows -> 32 PASS; wrote aih-tih-sc-1274d4-R1_A23YTGFLT4_1.arriba.fusions.filtered.tsv and aih-tih-sc-1274d4-R1_A23YTGFLT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: aih-tih-sc-1274d4-R1_A23YTGFLT4_1.arriba.fusions.filter_summary.txt