Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2f/eb06dae2d7f59334b8a0a1c597da99/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/51/810b0ec3f7e1a9d635ab60d382c837/tih_rna_sample_00161_B23WHTKLT4_2.arriba.fusions.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2f/eb06dae2d7f59334b8a0a1c597da99/.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-6a8e5f46-8592-47ae-b09e-a1efe7f02cb2/6a/80a8f8c27f6b00a3a33e35ea914965/arriba_filter_config.yaml
==> STAGING COMPLETE (5 inputs)

  AIH curated blacklist: matched 5 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 309
  Pass (FILTER=PASS): 56 (18.1%)
  Fail (FILTER=FAIL): 253 (81.9%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 5
  All 5 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 36
  confidence_below_min(medium<high);total_reads_below_min(6.0<8.0): 36
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 29
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 24
  confidence_below_min(medium<high): 23
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 17
  confidence_below_min(medium<high);total_reads_below_min(2.0<8.0): 12
  confidence_below_min(medium<high);total_reads_below_min(7.0<8.0): 12
  total_reads_below_min(6.0<8.0): 7
  confidence_below_min(low<high): 7
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 7
  total_reads_below_min(3.0<8.0): 6
  total_reads_below_min(5.0<8.0): 6
  total_reads_below_min(7.0<8.0): 6
  total_reads_below_min(4.0<8.0): 6

Breakdown by confidence:
  high: 56 pass, 32 fail (total: 88)
  low: 0 pass, 79 fail (total: 79)
  medium: 0 pass, 142 fail (total: 142)
Arriba filter: 309 rows -> 56 PASS; wrote tih_rna_sample_00161_B23WHTKLT4_2.arriba.fusions.filtered.tsv and tih_rna_sample_00161_B23WHTKLT4_2.arriba.fusions.filtered_pass_only.tsv
Summary written to: tih_rna_sample_00161_B23WHTKLT4_2.arriba.fusions.filter_summary.txt