Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/bb/58c31e35d50fe9850838fbb475bad5/659_cRB-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a3/895c8be9c20c9113b9354b5e644249/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a3/895c8be9c20c9113b9354b5e644249/.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-0c31b8cc-cacb-407a-8f2b-eb2d8317e249/e8/83b3d86dc9f1df6763490ba67ef20d/arriba_filter_config.yaml
==> STAGING COMPLETE (5 inputs)

  AIH curated blacklist: matched 10 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 120
  Pass (FILTER=PASS): 4 (3.3%)
  Fail (FILTER=FAIL): 116 (96.7%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 10
  All 10 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(medium<high): 25
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 15
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 15
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0): 11
  confidence_below_min(medium<high);total_reads_below_min(7.0<8.0): 10
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 8
  confidence_below_min(medium<high);aih_curated_blacklist: 5
  confidence_below_min(low<high): 4
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 3
  confidence_below_min(medium<high);total_reads_below_min(6.0<8.0): 3
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 3
  confidence_below_min(low<high);aih_curated_blacklist: 2
  confidence_below_min(low<high);total_reads_below_min(7.0<8.0): 2
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 2
  total_reads_below_min(5.0<8.0): 1

Breakdown by confidence:
  high: 4 pass, 2 fail (total: 6)
  low: 0 pass, 42 fail (total: 42)
  medium: 0 pass, 72 fail (total: 72)
Arriba filter: 120 rows -> 4 PASS; wrote 659_cRB-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.filtered.tsv and 659_cRB-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: 659_cRB-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.filter_summary.txt