Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2f/56bbf96ca1d553862383badc8f966c/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2f/56bbf96ca1d553862383badc8f966c/.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/36/c89e7da833c13635166b8c942fcc9c/659_Lx-T1-TRNA-1_A23MVY2LT4_2.arriba.fusions.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 5 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 155
  Pass (FILTER=PASS): 7 (4.5%)
  Fail (FILTER=FAIL): 148 (95.5%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 5
  All 5 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(medium<high): 61
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 16
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 13
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 10
  confidence_below_min(medium<high);total_reads_below_min(2.0<8.0): 10
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 6
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 6
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 5
  confidence_below_min(low<high): 5
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 4
  confidence_below_min(low<high);total_reads_below_min(6.0<8.0): 3
  confidence_below_min(medium<high);aih_curated_blacklist: 3
  aih_curated_blacklist: 1
  total_reads_below_min(6.0<8.0): 1
  total_reads_below_min(3.0<8.0): 1

Breakdown by confidence:
  high: 7 pass, 3 fail (total: 10)
  low: 0 pass, 48 fail (total: 48)
  medium: 0 pass, 97 fail (total: 97)
Arriba filter: 155 rows -> 7 PASS; wrote 659_Lx-T1-TRNA-1_A23MVY2LT4_2.arriba.fusions.filtered.tsv and 659_Lx-T1-TRNA-1_A23MVY2LT4_2.arriba.fusions.filtered_pass_only.tsv
Summary written to: 659_Lx-T1-TRNA-1_A23MVY2LT4_2.arriba.fusions.filter_summary.txt