Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/90/f706439cbb43db5a07390844fde267/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/90/f706439cbb43db5a07390844fde267/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c7/23b9f9009a7811d9f0d6c360cf68cb/tih_rna_sample_00096_B23WHTKLT4_2.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 8 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 246
  Pass (FILTER=PASS): 18 (7.3%)
  Fail (FILTER=FAIL): 228 (92.7%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 8
  All 8 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(medium<high): 58
  confidence_below_min(medium<high);total_reads_below_min(7.0<8.0): 25
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 24
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 18
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 17
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 17
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 16
  confidence_below_min(low<high): 16
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 6
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 6
  confidence_below_min(low<high);total_reads_below_min(7.0<8.0): 5
  confidence_below_min(medium<high);aih_curated_blacklist: 4
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 4
  confidence_below_min(medium<high);total_reads_below_min(6.0<8.0): 3
  total_reads_below_min(3.0<8.0): 2

Breakdown by confidence:
  high: 18 pass, 4 fail (total: 22)
  low: 0 pass, 110 fail (total: 110)
  medium: 0 pass, 114 fail (total: 114)
Arriba filter: 246 rows -> 18 PASS; wrote tih_rna_sample_00096_B23WHTKLT4_2.arriba.fusions.filtered.tsv and tih_rna_sample_00096_B23WHTKLT4_2.arriba.fusions.filtered_pass_only.tsv
Summary written to: tih_rna_sample_00096_B23WHTKLT4_2.arriba.fusions.filter_summary.txt