Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b7/46a64b1bd6fe46c0880ba8023466f1/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ba/9166a6bd251bfd1de75c0b32ebc92e/tih_rna_sample_00161_B23WHTKLT4_2.arriba.fusions.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b7/46a64b1bd6fe46c0880ba8023466f1/.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 6 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 395
  Pass (FILTER=PASS): 78 (19.7%)
  Fail (FILTER=FAIL): 317 (80.3%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 6
  All 6 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(medium<high): 55
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 46
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0): 28
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 27
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 23
  confidence_below_min(medium<high);total_reads_below_min(6.0<8.0): 22
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 22
  confidence_below_min(medium<high);total_reads_below_min(7.0<8.0): 16
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 15
  confidence_below_min(medium<high);total_reads_below_min(2.0<8.0): 11
  confidence_below_min(low<high): 9
  total_reads_below_min(3.0<8.0): 7
  total_reads_below_min(6.0<8.0): 7
  total_reads_below_min(4.0<8.0): 5
  total_reads_below_min(7.0<8.0): 4

Breakdown by confidence:
  high: 78 pass, 25 fail (total: 103)
  low: 0 pass, 111 fail (total: 111)
  medium: 0 pass, 181 fail (total: 181)
Arriba filter: 395 rows -> 78 PASS; wrote tih_rna_sample_00161_B23WHTKLT4_2.arriba.fusions.filtered.tsv and tih_rna_sample_00161_B23WHTKLT4_2.arriba.fusions.filtered_pass_only.tsv
Summary written to: tih_rna_sample_00161_B23WHTKLT4_2.arriba.fusions.filter_summary.txt