Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/90/6e4da56f5c5c6bfc3eaf0e8a13226b/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/90/6e4da56f5c5c6bfc3eaf0e8a13226b/.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/fd/a65f112e6b3ca7d5ec48e7801006e7/tih_rna_sample_00121_B23WHTKLT4_2.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 11 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 258
  Pass (FILTER=PASS): 27 (10.5%)
  Fail (FILTER=FAIL): 231 (89.5%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 11
  All 11 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(medium<high): 81
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 26
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 22
  confidence_below_min(low<high): 20
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 13
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 12
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 8
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0): 6
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 5
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 4
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 4
  total_reads_below_min(5.0<8.0): 4
  confidence_below_min(medium<high);total_reads_below_min(7.0<8.0): 4
  confidence_below_min(low<high);total_reads_below_min(6.0<8.0): 3
  total_reads_below_min(4.0<8.0): 3

Breakdown by confidence:
  high: 27 pass, 11 fail (total: 38)
  low: 0 pass, 108 fail (total: 108)
  medium: 0 pass, 112 fail (total: 112)
Arriba filter: 258 rows -> 27 PASS; wrote tih_rna_sample_00121_B23WHTKLT4_2.arriba.fusions.filtered.tsv and tih_rna_sample_00121_B23WHTKLT4_2.arriba.fusions.filtered_pass_only.tsv
Summary written to: tih_rna_sample_00121_B23WHTKLT4_2.arriba.fusions.filter_summary.txt