Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ab/e2fb27effa9ab677c6bdb470c2191a/659_cRa-T1-TRNA-1_A23MVY2LT4_2.arriba.fusions.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7c/e58e41933a3a439bd039eb6a4558f3/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7c/e58e41933a3a439bd039eb6a4558f3/.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-bba2394f-ea06-4038-829e-f0bb41c45b0f/84/e510984b93930338ae941c5c84bcbe/arriba_filter_config.yaml
==> STAGING COMPLETE (5 inputs)

  AIH curated blacklist: matched 7 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 226
  Pass (FILTER=PASS): 9 (4.0%)
  Fail (FILTER=FAIL): 217 (96.0%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 7
  All 7 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(medium<high): 47
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 31
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 23
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 20
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 16
  confidence_below_min(medium<high);total_reads_below_min(6.0<8.0): 13
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 13
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 11
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 5
  confidence_below_min(medium<high);total_reads_below_min(2.0<8.0): 5
  confidence_below_min(medium<high);aih_curated_blacklist: 4
  confidence_below_min(low<high): 4
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0): 4
  total_reads_below_min(3.0<8.0): 4
  confidence_below_min(low<high);total_reads_below_min(6.0<8.0): 3

Breakdown by confidence:
  high: 9 pass, 9 fail (total: 18)
  low: 0 pass, 85 fail (total: 85)
  medium: 0 pass, 123 fail (total: 123)
Arriba filter: 226 rows -> 9 PASS; wrote 659_cRa-T1-TRNA-1_A23MVY2LT4_2.arriba.fusions.filtered.tsv and 659_cRa-T1-TRNA-1_A23MVY2LT4_2.arriba.fusions.filtered_pass_only.tsv
Summary written to: 659_cRa-T1-TRNA-1_A23MVY2LT4_2.arriba.fusions.filter_summary.txt