Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/cd/b708212dc36a83a2ccfa87dcdeebb9/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9b/31166f81d081868216d844d4b74c61/tih_rna_sample_00089_B23WHTKLT4_1.arriba.fusions.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/cd/b708212dc36a83a2ccfa87dcdeebb9/.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 6 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 161
  Pass (FILTER=PASS): 17 (10.6%)
  Fail (FILTER=FAIL): 144 (89.4%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 6
  All 6 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0): 22
  confidence_below_min(medium<high): 19
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 16
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 13
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 12
  confidence_below_min(medium<high);total_reads_below_min(7.0<8.0): 11
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 10
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 6
  confidence_below_min(low<high);total_reads_below_min(7.0<8.0): 5
  confidence_below_min(medium<high);total_reads_below_min(2.0<8.0): 5
  confidence_below_min(low<high): 5
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 3
  total_reads_below_min(3.0<8.0): 2
  total_reads_below_min(6.0<8.0): 2
  confidence_below_min(medium<high);aih_curated_blacklist: 2

Breakdown by confidence:
  high: 17 pass, 9 fail (total: 26)
  low: 0 pass, 61 fail (total: 61)
  medium: 0 pass, 74 fail (total: 74)
Arriba filter: 161 rows -> 17 PASS; wrote tih_rna_sample_00089_B23WHTKLT4_1.arriba.fusions.filtered.tsv and tih_rna_sample_00089_B23WHTKLT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: tih_rna_sample_00089_B23WHTKLT4_1.arriba.fusions.filter_summary.txt