Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d8/97d4fad83768c74526fca83f188989/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d8/97d4fad83768c74526fca83f188989/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6a/05e7252138beed3be8e9110e022c5b/tih_rna_sample_00678_B23MVV7LT4_1.arriba.fusions.tsv
  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-7324c8a8-f474-426a-a5c9-715912777f94/d8/92d6652b0b8fcc763d0f3fff270437/arriba_filter_config.yaml
==> STAGING COMPLETE (5 inputs)

  AIH curated blacklist: matched 3 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 87
  Pass (FILTER=PASS): 1 (1.1%)
  Fail (FILTER=FAIL): 86 (98.9%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 3
  All 3 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 20
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 13
  confidence_below_min(medium<high);total_reads_below_min(7.0<8.0): 10
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0): 10
  confidence_below_min(low<high): 8
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 6
  confidence_below_min(medium<high): 5
  confidence_below_min(medium<high);aih_curated_blacklist: 3
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 2
  confidence_below_min(medium<high);total_reads_below_min(2.0<8.0): 2
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 2
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 2
  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(1.0<8.0): 1

Breakdown by confidence:
  high: 1 pass, 0 fail (total: 1)
  low: 0 pass, 23 fail (total: 23)
  medium: 0 pass, 63 fail (total: 63)
Arriba filter: 87 rows -> 1 PASS; wrote tih_rna_sample_00678_B23MVV7LT4_1.arriba.fusions.filtered.tsv and tih_rna_sample_00678_B23MVV7LT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: tih_rna_sample_00678_B23MVV7LT4_1.arriba.fusions.filter_summary.txt