Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c1/b65a34e3041cf9fc4d8f1d37021325/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c1/b65a34e3041cf9fc4d8f1d37021325/.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/c6/0a77817fb092adfd9080257c2a7b6d/FFPE_V4_0002_RNA_0001_B23MVV7LT4_1.arriba.fusions.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/stage-7324c8a8-f474-426a-a5c9-715912777f94/d8/92d6652b0b8fcc763d0f3fff270437/arriba_filter_config.yaml
==> STAGING COMPLETE (5 inputs)

  AIH curated blacklist: matched 9 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 122
  Pass (FILTER=PASS): 19 (15.6%)
  Fail (FILTER=FAIL): 103 (84.4%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 9
  All 9 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 14
  confidence_below_min(low<high): 11
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 11
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 10
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 9
  confidence_below_min(medium<high): 9
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 8
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 7
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 6
  confidence_below_min(medium<high);aih_curated_blacklist: 3
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 3
  confidence_below_min(medium<high);total_reads_below_min(2.0<8.0): 3
  confidence_below_min(low<high);total_reads_below_min(6.0<8.0): 2
  aih_curated_blacklist: 2
  total_reads_below_min(4.0<8.0);aih_curated_blacklist: 1

Breakdown by confidence:
  high: 19 pass, 3 fail (total: 22)
  low: 0 pass, 73 fail (total: 73)
  medium: 0 pass, 27 fail (total: 27)
Arriba filter: 122 rows -> 19 PASS; wrote FFPE_V4_0002_RNA_0001_B23MVV7LT4_1.arriba.fusions.filtered.tsv and FFPE_V4_0002_RNA_0001_B23MVV7LT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: FFPE_V4_0002_RNA_0001_B23MVV7LT4_1.arriba.fusions.filter_summary.txt