Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e8/2a77c0d1fa4cf4a516eebbb786d792/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e8/2a77c0d1fa4cf4a516eebbb786d792/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fd/757296e58c6be0566ca11bd2b9adb9/659_rd-T1-TRNA-1_A23MVY2LT4_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-bba2394f-ea06-4038-829e-f0bb41c45b0f/84/e510984b93930338ae941c5c84bcbe/arriba_filter_config.yaml
==> STAGING COMPLETE (5 inputs)

  AIH curated blacklist: matched 11 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 315
  Pass (FILTER=PASS): 39 (12.4%)
  Fail (FILTER=FAIL): 276 (87.6%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 11
  All 11 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(medium<high): 81
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 45
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 32
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 22
  confidence_below_min(low<high): 21
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 15
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 13
  confidence_below_min(low<high);total_reads_below_min(6.0<8.0): 8
  confidence_below_min(medium<high);total_reads_below_min(2.0<8.0): 7
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 7
  confidence_below_min(medium<high);aih_curated_blacklist: 5
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 5
  confidence_below_min(medium<high);total_reads_below_min(6.0<8.0): 3
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 3
  aih_curated_blacklist: 2

Breakdown by confidence:
  high: 39 pass, 3 fail (total: 42)
  low: 0 pass, 164 fail (total: 164)
  medium: 0 pass, 109 fail (total: 109)
Arriba filter: 315 rows -> 39 PASS; wrote 659_rd-T1-TRNA-1_A23MVY2LT4_1.arriba.fusions.filtered.tsv and 659_rd-T1-TRNA-1_A23MVY2LT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: 659_rd-T1-TRNA-1_A23MVY2LT4_1.arriba.fusions.filter_summary.txt