Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f9/23a57472c1ece123b3231c8d37d723/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f9/23a57472c1ece123b3231c8d37d723/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/67/ef06cc62391adf1efa0c26ab4485e6/tih_rna_sample_00479_B23WHTKLT4_1.arriba.fusions.tsv
  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 8 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 315
  Pass (FILTER=PASS): 69 (21.9%)
  Fail (FILTER=FAIL): 246 (78.1%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 8
  All 8 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 41
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 34
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 26
  confidence_below_min(medium<high): 24
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 24
  confidence_below_min(medium<high);total_reads_below_min(2.0<8.0): 12
  confidence_below_min(low<high);total_reads_below_min(6.0<8.0): 10
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 8
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0): 8
  confidence_below_min(medium<high);total_reads_below_min(7.0<8.0): 6
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 6
  total_reads_below_min(5.0<8.0): 6
  confidence_below_min(low<high): 6
  total_reads_below_min(6.0<8.0): 5
  total_reads_below_min(7.0<8.0): 4

Breakdown by confidence:
  high: 69 pass, 21 fail (total: 90)
  low: 0 pass, 135 fail (total: 135)
  medium: 0 pass, 90 fail (total: 90)
Arriba filter: 315 rows -> 69 PASS; wrote tih_rna_sample_00479_B23WHTKLT4_1.arriba.fusions.filtered.tsv and tih_rna_sample_00479_B23WHTKLT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: tih_rna_sample_00479_B23WHTKLT4_1.arriba.fusions.filter_summary.txt