Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c0/d78b8600f1a8bc00a33419063abd3a/659_epP-T1-TRNA-1_A23MVY2LT4_1.arriba.fusions.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a7/80db2e3f2ac60cbc1d79a2d1fa3484/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a7/80db2e3f2ac60cbc1d79a2d1fa3484/.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 12 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 181
  Pass (FILTER=PASS): 11 (6.1%)
  Fail (FILTER=FAIL): 170 (93.9%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 12
  All 12 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0): 22
  confidence_below_min(medium<high): 17
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 17
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 17
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 12
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 11
  confidence_below_min(medium<high);total_reads_below_min(2.0<8.0): 11
  confidence_below_min(low<high): 10
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 9
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 9
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 5
  confidence_below_min(medium<high);aih_curated_blacklist: 5
  confidence_below_min(low<high);total_reads_below_min(7.0<8.0): 4
  confidence_below_min(low<high);total_reads_below_min(6.0<8.0): 4
  total_reads_below_min(3.0<8.0): 3

Breakdown by confidence:
  high: 11 pass, 7 fail (total: 18)
  low: 0 pass, 82 fail (total: 82)
  medium: 0 pass, 81 fail (total: 81)
Arriba filter: 181 rows -> 11 PASS; wrote 659_epP-T1-TRNA-1_A23MVY2LT4_1.arriba.fusions.filtered.tsv and 659_epP-T1-TRNA-1_A23MVY2LT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: 659_epP-T1-TRNA-1_A23MVY2LT4_1.arriba.fusions.filter_summary.txt