Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/28/8845fa05e5df12ec225d8167d2b097/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/28/8845fa05e5df12ec225d8167d2b097/.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/c5/4507f8d99a9b4e4bcc7a521ba68019/aih-tih-sc-598a93-R1_A23YTGFLT4_1.arriba.fusions.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/stage-e543dae6-5fea-4720-bfb6-150bf1ff20d4/33/a04540cea7c8abc13163bc03b147d5/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: 18
  Pass (FILTER=PASS): 0 (0.0%)
  Fail (FILTER=FAIL): 18 (100.0%)

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

Failure reasons (top 15):
  confidence_below_min(medium<high);aih_curated_blacklist: 4
  confidence_below_min(medium<high);total_reads_below_min(2.0<8.0): 4
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 2
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 2
  total_reads_below_min(5.0<8.0): 1
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0);aih_curated_blacklist: 1
  confidence_below_min(low<high): 1
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 1
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 1
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0);aih_curated_blacklist: 1

Breakdown by confidence:
  high: 0 pass, 1 fail (total: 1)
  low: 0 pass, 6 fail (total: 6)
  medium: 0 pass, 11 fail (total: 11)
Arriba filter: 18 rows -> 0 PASS; wrote aih-tih-sc-598a93-R1_A23YTGFLT4_1.arriba.fusions.filtered.tsv and aih-tih-sc-598a93-R1_A23YTGFLT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: aih-tih-sc-598a93-R1_A23YTGFLT4_1.arriba.fusions.filter_summary.txt