Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/65/9b828cfafb33d0fc10897059c7b8bb/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/65/9b828cfafb33d0fc10897059c7b8bb/.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/97/48239e9d71194f1ae5bb8f22439e38/659_cRB-T1-TRNA-1_B23WHTKLT4_1.arriba.fusions.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/stage-99ebc9bd-f9f1-4b2c-b9a0-02ddaf99f257/ee/adda01b2d23fdd27de06edfd21ea26/arriba_filter_config.yaml
==> STAGING COMPLETE (5 inputs)

  AIH curated blacklist: matched 5 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 59
  Pass (FILTER=PASS): 1 (1.7%)
  Fail (FILTER=FAIL): 58 (98.3%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 5
  All 5 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 11
  confidence_below_min(medium<high): 10
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 8
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 5
  confidence_below_min(medium<high);aih_curated_blacklist: 4
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 3
  confidence_below_min(low<high);total_reads_below_min(7.0<8.0): 3
  confidence_below_min(low<high);total_reads_below_min(6.0<8.0): 3
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 3
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 2
  total_reads_below_min(6.0<8.0): 1
  total_reads_below_min(4.0<8.0): 1
  confidence_below_min(medium<high);total_reads_below_min(2.0<8.0): 1
  confidence_below_min(low<high): 1
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 1

Breakdown by confidence:
  high: 1 pass, 2 fail (total: 3)
  low: 0 pass, 27 fail (total: 27)
  medium: 0 pass, 29 fail (total: 29)
Arriba filter: 59 rows -> 1 PASS; wrote 659_cRB-T1-TRNA-1_B23WHTKLT4_1.arriba.fusions.filtered.tsv and 659_cRB-T1-TRNA-1_B23WHTKLT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: 659_cRB-T1-TRNA-1_B23WHTKLT4_1.arriba.fusions.filter_summary.txt