Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f1/2d279dfa5833cd085227cf65638e89/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f1/2d279dfa5833cd085227cf65638e89/.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/ad/0e04ee4f4ae9f7fc2143796eedaaea/aih-tih-sc-573e21-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 8 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 301
  Pass (FILTER=PASS): 10 (3.3%)
  Fail (FILTER=FAIL): 291 (96.7%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 8
  All 8 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 67
  confidence_below_min(medium<high): 59
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 26
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 21
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 17
  confidence_below_min(medium<high);total_reads_below_min(2.0<8.0): 16
  confidence_below_min(low<high): 16
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 14
  confidence_below_min(medium<high);total_reads_below_min(6.0<8.0): 11
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 6
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 6
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 5
  confidence_below_min(medium<high);total_reads_below_min(7.0<8.0): 4
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0): 4
  confidence_below_min(medium<high);aih_curated_blacklist: 3

Breakdown by confidence:
  high: 10 pass, 5 fail (total: 15)
  low: 0 pass, 151 fail (total: 151)
  medium: 0 pass, 135 fail (total: 135)
Arriba filter: 301 rows -> 10 PASS; wrote aih-tih-sc-573e21-R1_A23YTGFLT4_1.arriba.fusions.filtered.tsv and aih-tih-sc-573e21-R1_A23YTGFLT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: aih-tih-sc-573e21-R1_A23YTGFLT4_1.arriba.fusions.filter_summary.txt