Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/32/2d941da2e3f9c4e1763d313c732306/tih_rna_sample_00461_B23WHTKLT4_2.arriba.fusions.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/08/b074a80eb24e8c8280464bd2048403/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/08/b074a80eb24e8c8280464bd2048403/.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 2 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 272
  Pass (FILTER=PASS): 51 (18.8%)
  Fail (FILTER=FAIL): 221 (81.2%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 2
  All 2 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): 29
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 28
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 25
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 18
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 11
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0): 10
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 8
  confidence_below_min(low<high): 7
  confidence_below_min(medium<high);total_reads_below_min(2.0<8.0): 7
  total_reads_below_min(5.0<8.0): 6
  confidence_below_min(medium<high);total_reads_below_min(6.0<8.0): 5
  total_reads_below_min(4.0<8.0): 5
  total_reads_below_min(3.0<8.0): 4
  confidence_below_min(medium<high);total_reads_below_min(7.0<8.0): 4

Breakdown by confidence:
  high: 51 pass, 22 fail (total: 73)
  low: 0 pass, 100 fail (total: 100)
  medium: 0 pass, 99 fail (total: 99)
Arriba filter: 272 rows -> 51 PASS; wrote tih_rna_sample_00461_B23WHTKLT4_2.arriba.fusions.filtered.tsv and tih_rna_sample_00461_B23WHTKLT4_2.arriba.fusions.filtered_pass_only.tsv
Summary written to: tih_rna_sample_00461_B23WHTKLT4_2.arriba.fusions.filter_summary.txt