Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/64/3a20109d8bb2e6ab1d93816043bb48/tih_rna_sample_00146_B23WHTKLT4_2.arriba.fusions.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/61/a77a606b2d47dd1adb244f36e20dc4/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/61/a77a606b2d47dd1adb244f36e20dc4/.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 7 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 189
  Pass (FILTER=PASS): 10 (5.3%)
  Fail (FILTER=FAIL): 179 (94.7%)

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

Failure reasons (top 15):
  confidence_below_min(medium<high): 68
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 15
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 14
  confidence_below_min(low<high);total_reads_below_min(7.0<8.0): 11
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 9
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 9
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 7
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 7
  confidence_below_min(low<high): 7
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 6
  confidence_below_min(medium<high);total_reads_below_min(2.0<8.0): 4
  confidence_below_min(medium<high);total_reads_below_min(6.0<8.0): 4
  confidence_below_min(low<high);total_reads_below_min(6.0<8.0): 3
  total_reads_below_min(7.0<8.0): 2
  aih_curated_blacklist: 2

Breakdown by confidence:
  high: 10 pass, 6 fail (total: 16)
  low: 0 pass, 71 fail (total: 71)
  medium: 0 pass, 102 fail (total: 102)
Arriba filter: 189 rows -> 10 PASS; wrote tih_rna_sample_00146_B23WHTKLT4_2.arriba.fusions.filtered.tsv and tih_rna_sample_00146_B23WHTKLT4_2.arriba.fusions.filtered_pass_only.tsv
Summary written to: tih_rna_sample_00146_B23WHTKLT4_2.arriba.fusions.filter_summary.txt