Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e6/ad94bdffd9c990b09d4123d36bcd1b/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e6/ad94bdffd9c990b09d4123d36bcd1b/.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/c9/b73bbe2c40cacc0cc16edb30ed7df2/tih_rna_sample_00473_B23WHTKLT4_2.arriba.fusions.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 4 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 150
  Pass (FILTER=PASS): 8 (5.3%)
  Fail (FILTER=FAIL): 142 (94.7%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 4
  All 4 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0): 23
  confidence_below_min(medium<high): 22
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 16
  confidence_below_min(medium<high);total_reads_below_min(6.0<8.0): 12
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 10
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 9
  confidence_below_min(low<high): 9
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 7
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 6
  confidence_below_min(medium<high);total_reads_below_min(2.0<8.0): 4
  confidence_below_min(low<high);total_reads_below_min(5.0<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
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 3
  total_reads_below_min(5.0<8.0): 2

Breakdown by confidence:
  high: 8 pass, 6 fail (total: 14)
  low: 0 pass, 58 fail (total: 58)
  medium: 0 pass, 78 fail (total: 78)
Arriba filter: 150 rows -> 8 PASS; wrote tih_rna_sample_00473_B23WHTKLT4_2.arriba.fusions.filtered.tsv and tih_rna_sample_00473_B23WHTKLT4_2.arriba.fusions.filtered_pass_only.tsv
Summary written to: tih_rna_sample_00473_B23WHTKLT4_2.arriba.fusions.filter_summary.txt