Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/93/b90c3dd757ecea1f57b84a0117874e/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/93/b90c3dd757ecea1f57b84a0117874e/.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/f3/aba80828b4eb6889557797b3038f28/aih-tih-sc-82e8c1-R1_B23WHYVLT4_1.arriba.fusions.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/stage-8900cb43-4dca-49ac-a290-1d176a2e0012/49/8453bafeca2d0250d89cdefd7ba73e/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: 321
  Pass (FILTER=PASS): 55 (17.1%)
  Fail (FILTER=FAIL): 266 (82.9%)

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

Failure reasons (top 15):
  confidence_below_min(medium<high): 67
  confidence_below_min(low<high): 59
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 34
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 16
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 15
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 14
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 11
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 8
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 7
  confidence_below_min(medium<high);total_reads_below_min(7.0<8.0): 7
  confidence_below_min(low<high);total_reads_below_min(6.0<8.0): 6
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 6
  confidence_below_min(low<high);total_reads_below_min(7.0<8.0): 6
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0): 3
  confidence_below_min(medium<high);aih_curated_blacklist: 2

Breakdown by confidence:
  high: 55 pass, 2 fail (total: 57)
  low: 0 pass, 164 fail (total: 164)
  medium: 0 pass, 100 fail (total: 100)
Arriba filter: 321 rows -> 55 PASS; wrote aih-tih-sc-82e8c1-R1_B23WHYVLT4_1.arriba.fusions.filtered.tsv and aih-tih-sc-82e8c1-R1_B23WHYVLT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: aih-tih-sc-82e8c1-R1_B23WHYVLT4_1.arriba.fusions.filter_summary.txt