Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a8/2d8e9c3df3c9ed9bb368bf08fc27f2/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a8/2d8e9c3df3c9ed9bb368bf08fc27f2/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/21/e45e8c25fb97b4b01b541b1dcf51bb/659_bTo-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 9 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 269
  Pass (FILTER=PASS): 30 (11.2%)
  Fail (FILTER=FAIL): 239 (88.8%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 9
  All 9 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(medium<high): 86
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 36
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 17
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 16
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 15
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 13
  confidence_below_min(low<high): 10
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 9
  confidence_below_min(medium<high);total_reads_below_min(6.0<8.0): 6
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0): 5
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 5
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 4
  confidence_below_min(medium<high);aih_curated_blacklist: 3
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0);aih_curated_blacklist: 2
  confidence_below_min(medium<high);total_reads_below_min(2.0<8.0): 2

Breakdown by confidence:
  high: 30 pass, 3 fail (total: 33)
  low: 0 pass, 113 fail (total: 113)
  medium: 0 pass, 123 fail (total: 123)
Arriba filter: 269 rows -> 30 PASS; wrote 659_bTo-T1-TRNA-1_A23MVY2LT4_1.arriba.fusions.filtered.tsv and 659_bTo-T1-TRNA-1_A23MVY2LT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: 659_bTo-T1-TRNA-1_A23MVY2LT4_1.arriba.fusions.filter_summary.txt