Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/db/804b0879ccf83a4dce647b28863a20/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/db/804b0879ccf83a4dce647b28863a20/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/07/f675621e8c40f2b822dc5b7fab1c9f/659_bGW-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 16 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 260
  Pass (FILTER=PASS): 26 (10.0%)
  Fail (FILTER=FAIL): 234 (90.0%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 16
  All 16 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(medium<high): 103
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 20
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 17
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 11
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 10
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 9
  confidence_below_min(low<high): 9
  confidence_below_min(medium<high);aih_curated_blacklist: 7
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 7
  confidence_below_min(low<high);total_reads_below_min(6.0<8.0): 6
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 6
  confidence_below_min(medium<high);total_reads_below_min(6.0<8.0): 5
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 4
  confidence_below_min(medium<high);total_reads_below_min(2.0<8.0): 3
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0);aih_curated_blacklist: 3

Breakdown by confidence:
  high: 26 pass, 3 fail (total: 29)
  low: 0 pass, 90 fail (total: 90)
  medium: 0 pass, 141 fail (total: 141)
Arriba filter: 260 rows -> 26 PASS; wrote 659_bGW-T1-TRNA-1_A23MVY2LT4_1.arriba.fusions.filtered.tsv and 659_bGW-T1-TRNA-1_A23MVY2LT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: 659_bGW-T1-TRNA-1_A23MVY2LT4_1.arriba.fusions.filter_summary.txt