Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/33/0077211ec94c2d4fae3e10b84a2713/tih_rna_sample_00467_B23WHTKLT4_2.arriba.fusions.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/92/eb843d3db17c7d6058a47f07cf3427/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/92/eb843d3db17c7d6058a47f07cf3427/.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: 137
  Pass (FILTER=PASS): 8 (5.8%)
  Fail (FILTER=FAIL): 129 (94.2%)

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

Failure reasons (top 15):
  confidence_below_min(medium<high): 49
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 14
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 11
  confidence_below_min(medium<high);total_reads_below_min(6.0<8.0): 11
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 11
  confidence_below_min(low<high): 10
  confidence_below_min(medium<high);total_reads_below_min(2.0<8.0): 4
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 4
  confidence_below_min(medium<high);aih_curated_blacklist: 3
  total_reads_below_min(7.0<8.0): 1
  total_reads_below_min(6.0<8.0): 1
  total_reads_below_min(3.0<8.0): 1
  confidence_below_min(medium<high);total_reads_below_min(7.0<8.0): 1
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0): 1
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0);aih_curated_blacklist: 1

Breakdown by confidence:
  high: 8 pass, 3 fail (total: 11)
  low: 0 pass, 31 fail (total: 31)
  medium: 0 pass, 95 fail (total: 95)
Arriba filter: 137 rows -> 8 PASS; wrote tih_rna_sample_00467_B23WHTKLT4_2.arriba.fusions.filtered.tsv and tih_rna_sample_00467_B23WHTKLT4_2.arriba.fusions.filtered_pass_only.tsv
Summary written to: tih_rna_sample_00467_B23WHTKLT4_2.arriba.fusions.filter_summary.txt