Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f8/f0943b69f8cec663e7ecd9339d448e/tih_rna_sample_00136_B23WHTKLT4_1.arriba.fusions.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/18/a14cbd8fca3e5f805fdf2e447cebee/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/18/a14cbd8fca3e5f805fdf2e447cebee/.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 9 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 260
  Pass (FILTER=PASS): 32 (12.3%)
  Fail (FILTER=FAIL): 228 (87.7%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 9
  All 9 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(medium<high): 67
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 21
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 20
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 16
  confidence_below_min(medium<high);total_reads_below_min(6.0<8.0): 15
  confidence_below_min(low<high): 15
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0): 11
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 11
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 9
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 9
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 8
  total_reads_below_min(5.0<8.0): 4
  confidence_below_min(medium<high);aih_curated_blacklist: 4
  total_reads_below_min(3.0<8.0): 3
  confidence_below_min(medium<high);total_reads_below_min(7.0<8.0): 3

Breakdown by confidence:
  high: 32 pass, 10 fail (total: 42)
  low: 0 pass, 85 fail (total: 85)
  medium: 0 pass, 133 fail (total: 133)
Arriba filter: 260 rows -> 32 PASS; wrote tih_rna_sample_00136_B23WHTKLT4_1.arriba.fusions.filtered.tsv and tih_rna_sample_00136_B23WHTKLT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: tih_rna_sample_00136_B23WHTKLT4_1.arriba.fusions.filter_summary.txt