Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/97/54695169ff72afaa853d9b3d90f058/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4e/d890a0eed6953c9c9a6dec7fc2a7ff/tih_rna_sample_00754_B23MVV7LT4_1.arriba.fusions.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/97/54695169ff72afaa853d9b3d90f058/.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-7324c8a8-f474-426a-a5c9-715912777f94/d8/92d6652b0b8fcc763d0f3fff270437/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: 317
  Pass (FILTER=PASS): 49 (15.5%)
  Fail (FILTER=FAIL): 268 (84.5%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 8
  All 8 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(medium<high): 78
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 45
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 25
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 17
  confidence_below_min(low<high): 17
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 15
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 13
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 10
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0): 9
  confidence_below_min(medium<high);total_reads_below_min(6.0<8.0): 8
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 7
  confidence_below_min(medium<high);total_reads_below_min(7.0<8.0): 3
  confidence_below_min(low<high);total_reads_below_min(7.0<8.0): 3
  total_reads_below_min(7.0<8.0): 2
  total_reads_below_min(3.0<8.0): 2

Breakdown by confidence:
  high: 49 pass, 8 fail (total: 57)
  low: 0 pass, 126 fail (total: 126)
  medium: 0 pass, 134 fail (total: 134)
Arriba filter: 317 rows -> 49 PASS; wrote tih_rna_sample_00754_B23MVV7LT4_1.arriba.fusions.filtered.tsv and tih_rna_sample_00754_B23MVV7LT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: tih_rna_sample_00754_B23MVV7LT4_1.arriba.fusions.filter_summary.txt