Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ba/e22c509795019645e2674d104a52df/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ba/e22c509795019645e2674d104a52df/.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/7b/ab947690e085fbf9f9fdc17f1cee0d/659_beZ_T1_TRNA_2_B2372Y3LT4_1.arriba.fusions.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 4 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 39
  Pass (FILTER=PASS): 0 (0.0%)
  Fail (FILTER=FAIL): 39 (100.0%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 4
  All 4 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(medium<high);total_reads_below_min(2.0<8.0): 15
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 5
  confidence_below_min(medium<high);aih_curated_blacklist: 3
  total_reads_below_min(2.0<8.0): 2
  confidence_below_min(low<high): 2
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 2
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 2
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 2
  total_reads_below_min(4.0<8.0): 1
  confidence_below_min(medium<high): 1
  confidence_below_min(low<high);aih_curated_blacklist: 1
  confidence_below_min(low<high);total_reads_below_min(7.0<8.0): 1
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 1
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 1

Breakdown by confidence:
  high: 0 pass, 3 fail (total: 3)
  low: 0 pass, 17 fail (total: 17)
  medium: 0 pass, 19 fail (total: 19)
Arriba filter: 39 rows -> 0 PASS; wrote 659_beZ_T1_TRNA_2_B2372Y3LT4_1.arriba.fusions.filtered.tsv and 659_beZ_T1_TRNA_2_B2372Y3LT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: 659_beZ_T1_TRNA_2_B2372Y3LT4_1.arriba.fusions.filter_summary.txt