Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c7/c740a584c7778cd919d9f2ac69d941/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ec/4014a18fce81354c157319b185d589/tih_rna_sample_00150_B23WHTKLT4_1.arriba.fusions.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c7/c740a584c7778cd919d9f2ac69d941/.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 4 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 157
  Pass (FILTER=PASS): 8 (5.1%)
  Fail (FILTER=FAIL): 149 (94.9%)

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

Failure reasons (top 15):
  confidence_below_min(medium<high): 50
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 18
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 14
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 12
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 10
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 7
  confidence_below_min(low<high): 7
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 5
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0): 5
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 5
  confidence_below_min(low<high);total_reads_below_min(6.0<8.0): 3
  confidence_below_min(medium<high);total_reads_below_min(6.0<8.0): 3
  confidence_below_min(low<high);total_reads_below_min(7.0<8.0): 3
  confidence_below_min(medium<high);aih_curated_blacklist: 2
  total_reads_below_min(3.0<8.0): 1

Breakdown by confidence:
  high: 8 pass, 1 fail (total: 9)
  low: 0 pass, 79 fail (total: 79)
  medium: 0 pass, 69 fail (total: 69)
Arriba filter: 157 rows -> 8 PASS; wrote tih_rna_sample_00150_B23WHTKLT4_1.arriba.fusions.filtered.tsv and tih_rna_sample_00150_B23WHTKLT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: tih_rna_sample_00150_B23WHTKLT4_1.arriba.fusions.filter_summary.txt