Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/cb/7570fdae3da6ae43e201e362dfa7c9/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/cb/7570fdae3da6ae43e201e362dfa7c9/.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/41/67d5a7ba163b204ed914181ea491b9/659_cAd-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 10 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 198
  Pass (FILTER=PASS): 12 (6.1%)
  Fail (FILTER=FAIL): 186 (93.9%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 10
  All 10 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(medium<high): 30
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 27
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 24
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 23
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 21
  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): 8
  confidence_below_min(low<high): 5
  confidence_below_min(low<high);total_reads_below_min(6.0<8.0): 5
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 4
  confidence_below_min(medium<high);aih_curated_blacklist: 4
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0): 4
  confidence_below_min(low<high);total_reads_below_min(7.0<8.0): 4
  confidence_below_min(medium<high);total_reads_below_min(6.0<8.0): 3
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 3

Breakdown by confidence:
  high: 12 pass, 1 fail (total: 13)
  low: 0 pass, 95 fail (total: 95)
  medium: 0 pass, 90 fail (total: 90)
Arriba filter: 198 rows -> 12 PASS; wrote 659_cAd-T1-TRNA-1_A23MVY2LT4_2.arriba.fusions.filtered.tsv and 659_cAd-T1-TRNA-1_A23MVY2LT4_2.arriba.fusions.filtered_pass_only.tsv
Summary written to: 659_cAd-T1-TRNA-1_A23MVY2LT4_2.arriba.fusions.filter_summary.txt