Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/cf/781325ae3c7840d89847e43a7b20cd/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/cf/781325ae3c7840d89847e43a7b20cd/.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/14/c6c7c02cf1648ccd5d2d30fda03df6/BVT_FFPE_TRNA_stm_09_A23WKFTLT4_3.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 7 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 131
  Pass (FILTER=PASS): 27 (20.6%)
  Fail (FILTER=FAIL): 104 (79.4%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 7
  All 7 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(medium<high): 18
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 9
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 8
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 7
  total_reads_below_min(5.0<8.0): 6
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 6
  confidence_below_min(low<high): 6
  total_reads_below_min(4.0<8.0): 5
  confidence_below_min(medium<high);aih_curated_blacklist: 5
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 5
  confidence_below_min(medium<high);total_reads_below_min(6.0<8.0): 4
  confidence_below_min(medium<high);total_reads_below_min(7.0<8.0): 4
  confidence_below_min(low<high);total_reads_below_min(7.0<8.0): 4
  total_reads_below_min(3.0<8.0): 3
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 3

Breakdown by confidence:
  high: 27 pass, 15 fail (total: 42)
  low: 0 pass, 42 fail (total: 42)
  medium: 0 pass, 47 fail (total: 47)
Arriba filter: 131 rows -> 27 PASS; wrote BVT_FFPE_TRNA_stm_09_A23WKFTLT4_3.arriba.fusions.filtered.tsv and BVT_FFPE_TRNA_stm_09_A23WKFTLT4_3.arriba.fusions.filtered_pass_only.tsv
Summary written to: BVT_FFPE_TRNA_stm_09_A23WKFTLT4_3.arriba.fusions.filter_summary.txt