Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ea/e4ed67af89dd2b0c8ee8f80c9dd87d/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ea/e4ed67af89dd2b0c8ee8f80c9dd87d/.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/54/1c5e4ff5c4ac37f38c4be3f9c32d08/dna_s769.arriba.fusions.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/stage-fff52061-f714-4c14-bb2c-bf5549840817/43/06b80417dcdedb0d1513f19552f633/arriba_filter_config.yaml
==> STAGING COMPLETE (5 inputs)

  AIH curated blacklist: matched 3 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 74
  Pass (FILTER=PASS): 1 (1.4%)
  Fail (FILTER=FAIL): 73 (98.6%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 3
  All 3 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(medium<high): 33
  confidence_below_min(low<high): 12
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 6
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 4
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 3
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0): 3
  confidence_below_min(low<high);total_reads_below_min(6.0<8.0): 3
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 2
  confidence_below_min(low<high);total_reads_below_min(7.0<8.0): 2
  confidence_below_min(medium<high);aih_curated_blacklist: 1
  confidence_below_min(medium<high);total_reads_below_min(2.0<8.0);aih_curated_blacklist: 1
  confidence_below_min(low<high);total_reads_below_min(7.0<8.0);aih_curated_blacklist: 1
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 1
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 1

Breakdown by confidence:
  high: 1 pass, 0 fail (total: 1)
  low: 0 pass, 30 fail (total: 30)
  medium: 0 pass, 43 fail (total: 43)
Arriba filter: 74 rows -> 1 PASS; wrote dna_s769.arriba.fusions.filtered.tsv and dna_s769.arriba.fusions.filtered_pass_only.tsv
Summary written to: dna_s769.arriba.fusions.filter_summary.txt