Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ca/a9d6af7297320ec9ae9dcf0eda0a4d/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ca/a9d6af7297320ec9ae9dcf0eda0a4d/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3a/cebd5e6254e06a306995996d792c11/tih_rna_sample_00116_B23WHTKLT4_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-99ebc9bd-f9f1-4b2c-b9a0-02ddaf99f257/ee/adda01b2d23fdd27de06edfd21ea26/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: 82
  Pass (FILTER=PASS): 7 (8.5%)
  Fail (FILTER=FAIL): 75 (91.5%)

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

Failure reasons (top 15):
  confidence_below_min(medium<high): 19
  confidence_below_min(medium<high);total_reads_below_min(6.0<8.0): 10
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 9
  confidence_below_min(low<high): 6
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 6
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 3
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0): 3
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 3
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 3
  confidence_below_min(medium<high);aih_curated_blacklist: 2
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 2
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 2
  total_reads_below_min(5.0<8.0): 1
  total_reads_below_min(3.0<8.0): 1
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 1

Breakdown by confidence:
  high: 7 pass, 2 fail (total: 9)
  low: 0 pass, 32 fail (total: 32)
  medium: 0 pass, 41 fail (total: 41)
Arriba filter: 82 rows -> 7 PASS; wrote tih_rna_sample_00116_B23WHTKLT4_1.arriba.fusions.filtered.tsv and tih_rna_sample_00116_B23WHTKLT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: tih_rna_sample_00116_B23WHTKLT4_1.arriba.fusions.filter_summary.txt