Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1a/7d7ef534c0fca98ac126d21565d643/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1a/7d7ef534c0fca98ac126d21565d643/.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/22/e971a8c1d7066d7204d997ca7fa963/aih-tih-sc-bec563-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: 425
  Pass (FILTER=PASS): 62 (14.6%)
  Fail (FILTER=FAIL): 363 (85.4%)

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

Failure reasons (top 15):
  confidence_below_min(medium<high): 94
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 48
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 31
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 29
  confidence_below_min(medium<high);total_reads_below_min(7.0<8.0): 20
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 15
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 15
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0): 13
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 12
  confidence_below_min(low<high): 12
  confidence_below_min(medium<high);total_reads_below_min(6.0<8.0): 10
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 10
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 9
  confidence_below_min(low<high);total_reads_below_min(6.0<8.0): 7
  confidence_below_min(medium<high);total_reads_below_min(2.0<8.0): 6

Breakdown by confidence:
  high: 62 pass, 22 fail (total: 84)
  low: 0 pass, 133 fail (total: 133)
  medium: 0 pass, 208 fail (total: 208)
Arriba filter: 425 rows -> 62 PASS; wrote aih-tih-sc-bec563-R1_A23WJ53LT4_1.arriba.fusions.filtered.tsv and aih-tih-sc-bec563-R1_A23WJ53LT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: aih-tih-sc-bec563-R1_A23WJ53LT4_1.arriba.fusions.filter_summary.txt