Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d6/37de98986674989546a8220900501a/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6a/7bf84d53a512a9b58e340729104859/659_ciZ-T1-TRNA-1_B23WHTKLT4_1.arriba.fusions.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d6/37de98986674989546a8220900501a/.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-6a8e5f46-8592-47ae-b09e-a1efe7f02cb2/6a/80a8f8c27f6b00a3a33e35ea914965/arriba_filter_config.yaml
==> STAGING COMPLETE (5 inputs)

  AIH curated blacklist: matched 5 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 42
  Pass (FILTER=PASS): 4 (9.5%)
  Fail (FILTER=FAIL): 38 (90.5%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 5
  All 5 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 8
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 6
  confidence_below_min(medium<high);aih_curated_blacklist: 4
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 3
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 3
  confidence_below_min(low<high): 3
  confidence_below_min(medium<high): 2
  confidence_below_min(medium<high);total_reads_below_min(2.0<8.0): 2
  total_reads_below_min(2.0<8.0): 1
  confidence_below_min(medium<high);total_reads_below_min(6.0<8.0): 1
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0): 1
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0);aih_curated_blacklist: 1
  confidence_below_min(low<high);total_reads_below_min(6.0<8.0): 1
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 1
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 1

Breakdown by confidence:
  high: 4 pass, 1 fail (total: 5)
  low: 0 pass, 23 fail (total: 23)
  medium: 0 pass, 14 fail (total: 14)
Arriba filter: 42 rows -> 4 PASS; wrote 659_ciZ-T1-TRNA-1_B23WHTKLT4_1.arriba.fusions.filtered.tsv and 659_ciZ-T1-TRNA-1_B23WHTKLT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: 659_ciZ-T1-TRNA-1_B23WHTKLT4_1.arriba.fusions.filter_summary.txt