Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/eb/36f8a8f558d9de2c0aa7aa00a11844/tih_rna_sample_00161_B23WHTKLT4_1.arriba.fusions.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/de/fd99a79bbdbe47814029e6f9881199/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/de/fd99a79bbdbe47814029e6f9881199/.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/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: 305
  Pass (FILTER=PASS): 53 (17.4%)
  Fail (FILTER=FAIL): 252 (82.6%)

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

Failure reasons (top 15):
  confidence_below_min(medium<high): 40
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 36
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 34
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 33
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 19
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 17
  total_reads_below_min(6.0<8.0): 11
  confidence_below_min(low<high): 9
  total_reads_below_min(5.0<8.0): 7
  total_reads_below_min(4.0<8.0): 6
  confidence_below_min(medium<high);total_reads_below_min(2.0<8.0): 6
  total_reads_below_min(3.0<8.0): 6
  confidence_below_min(medium<high);total_reads_below_min(6.0<8.0): 5
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 4
  total_reads_below_min(7.0<8.0): 4

Breakdown by confidence:
  high: 53 pass, 34 fail (total: 87)
  low: 0 pass, 106 fail (total: 106)
  medium: 0 pass, 112 fail (total: 112)
Arriba filter: 305 rows -> 53 PASS; wrote tih_rna_sample_00161_B23WHTKLT4_1.arriba.fusions.filtered.tsv and tih_rna_sample_00161_B23WHTKLT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: tih_rna_sample_00161_B23WHTKLT4_1.arriba.fusions.filter_summary.txt