Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/af/8290c8e681a28d769e0ba12fd0ada7/aih-tih-sc-762402-R1_B23WHYVLT4_1.arriba.fusions.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/13/0d1865808d3e7e94d266c493b9f6d7/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/13/0d1865808d3e7e94d266c493b9f6d7/.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-8900cb43-4dca-49ac-a290-1d176a2e0012/49/8453bafeca2d0250d89cdefd7ba73e/arriba_filter_config.yaml
==> STAGING COMPLETE (5 inputs)

  AIH curated blacklist: matched 5 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 199
  Pass (FILTER=PASS): 31 (15.6%)
  Fail (FILTER=FAIL): 168 (84.4%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 5
  All 5 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(medium<high): 71
  confidence_below_min(low<high): 26
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 14
  confidence_below_min(medium<high);total_reads_below_min(6.0<8.0): 10
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 9
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 8
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 8
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 7
  confidence_below_min(medium<high);aih_curated_blacklist: 4
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 4
  confidence_below_min(low<high);total_reads_below_min(7.0<8.0): 2
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 2
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0);aih_curated_blacklist: 1
  confidence_below_min(medium<high);total_reads_below_min(2.0<8.0): 1
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 1

Breakdown by confidence:
  high: 31 pass, 0 fail (total: 31)
  low: 0 pass, 71 fail (total: 71)
  medium: 0 pass, 97 fail (total: 97)
Arriba filter: 199 rows -> 31 PASS; wrote aih-tih-sc-762402-R1_B23WHYVLT4_1.arriba.fusions.filtered.tsv and aih-tih-sc-762402-R1_B23WHYVLT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: aih-tih-sc-762402-R1_B23WHYVLT4_1.arriba.fusions.filter_summary.txt