Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2e/44032f9941a1d57695c87f526b3f97/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2e/44032f9941a1d57695c87f526b3f97/.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/5c/bb0e47002108519ef03cc4b07595cb/659_cWx-T1-TRNA-1_B23WHTKLT4_1.arriba.fusions.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 6 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 33
  Pass (FILTER=PASS): 3 (9.1%)
  Fail (FILTER=FAIL): 30 (90.9%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 6
  All 6 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 5
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 4
  confidence_below_min(medium<high): 3
  confidence_below_min(medium<high);aih_curated_blacklist: 3
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 3
  confidence_below_min(medium<high);total_reads_below_min(2.0<8.0): 3
  total_reads_below_min(2.0<8.0): 2
  confidence_below_min(low<high): 2
  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(1.0<8.0);aih_curated_blacklist: 1
  confidence_below_min(low<high);aih_curated_blacklist: 1
  confidence_below_min(low<high);total_reads_below_min(7.0<8.0): 1
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 1

Breakdown by confidence:
  high: 3 pass, 2 fail (total: 5)
  low: 0 pass, 15 fail (total: 15)
  medium: 0 pass, 13 fail (total: 13)
Arriba filter: 33 rows -> 3 PASS; wrote 659_cWx-T1-TRNA-1_B23WHTKLT4_1.arriba.fusions.filtered.tsv and 659_cWx-T1-TRNA-1_B23WHTKLT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: 659_cWx-T1-TRNA-1_B23WHTKLT4_1.arriba.fusions.filter_summary.txt