Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/52/7941dfe91c7327378e0af9e427d9e5/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/52/7941dfe91c7327378e0af9e427d9e5/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/38/790e45628a105bbcd63e127efcd9fe/659_w_T1_TRNA_1_B2372Y3LT4_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-fff52061-f714-4c14-bb2c-bf5549840817/43/06b80417dcdedb0d1513f19552f633/arriba_filter_config.yaml
==> STAGING COMPLETE (5 inputs)

  AIH curated blacklist: matched 3 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 52
  Pass (FILTER=PASS): 1 (1.9%)
  Fail (FILTER=FAIL): 51 (98.1%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 3
  All 3 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(medium<high): 10
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 9
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 7
  confidence_below_min(low<high): 7
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 4
  confidence_below_min(medium<high);aih_curated_blacklist: 2
  confidence_below_min(medium<high);total_reads_below_min(7.0<8.0): 2
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 2
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 2
  aih_curated_blacklist: 1
  total_reads_below_min(5.0<8.0): 1
  total_reads_below_min(4.0<8.0): 1
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 1
  confidence_below_min(medium<high);total_reads_below_min(2.0<8.0): 1
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 1

Breakdown by confidence:
  high: 1 pass, 3 fail (total: 4)
  low: 0 pass, 31 fail (total: 31)
  medium: 0 pass, 17 fail (total: 17)
Arriba filter: 52 rows -> 1 PASS; wrote 659_w_T1_TRNA_1_B2372Y3LT4_1.arriba.fusions.filtered.tsv and 659_w_T1_TRNA_1_B2372Y3LT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: 659_w_T1_TRNA_1_B2372Y3LT4_1.arriba.fusions.filter_summary.txt