Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a6/0b38520bb3e5f480389d727818a00a/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a6/0b38520bb3e5f480389d727818a00a/.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/ef/25e2f46cf2defe6277c595a94fc5f4/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_2.arriba.fusions.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/stage-13dfb8f7-c999-4ef0-9260-22ba79cf647d/75/c52a23060671398a8253a658f32ecc/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: 141
  Pass (FILTER=PASS): 9 (6.4%)
  Fail (FILTER=FAIL): 132 (93.6%)

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(0.0<8.0): 23
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 20
  confidence_below_min(low<high): 18
  confidence_below_min(medium<high): 16
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 13
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 12
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 6
  confidence_below_min(low<high);total_reads_below_min(7.0<8.0): 4
  confidence_below_min(medium<high);aih_curated_blacklist: 4
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 3
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 3
  confidence_below_min(medium<high);total_reads_below_min(6.0<8.0): 2
  aih_curated_blacklist: 1
  total_reads_below_min(3.0<8.0);aih_curated_blacklist: 1
  confidence_below_min(medium<high);total_reads_below_min(7.0<8.0): 1

Breakdown by confidence:
  high: 9 pass, 2 fail (total: 11)
  low: 0 pass, 98 fail (total: 98)
  medium: 0 pass, 32 fail (total: 32)
Arriba filter: 141 rows -> 9 PASS; wrote BVT_FFPE_TRNA_bld_02_A23WKFTLT4_2.arriba.fusions.filtered.tsv and BVT_FFPE_TRNA_bld_02_A23WKFTLT4_2.arriba.fusions.filtered_pass_only.tsv
Summary written to: BVT_FFPE_TRNA_bld_02_A23WKFTLT4_2.arriba.fusions.filter_summary.txt