Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e4/ed14acaa0910d7e1f72c8559a253dc/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e4/ed14acaa0910d7e1f72c8559a253dc/.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/5a/22a4d49a315f513efa9f8215ebd33c/FFPE_HD789_01_RNA_13_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 12 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 443
  Pass (FILTER=PASS): 59 (13.3%)
  Fail (FILTER=FAIL): 384 (86.7%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 12
  All 12 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 78
  confidence_below_min(medium<high): 64
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0): 35
  confidence_below_min(low<high): 26
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 24
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 22
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 20
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 18
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 18
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 17
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 10
  confidence_below_min(low<high);total_reads_below_min(6.0<8.0): 10
  confidence_below_min(medium<high);total_reads_below_min(2.0<8.0): 9
  confidence_below_min(medium<high);aih_curated_blacklist: 5
  confidence_below_min(low<high);total_reads_below_min(7.0<8.0): 5

Breakdown by confidence:
  high: 59 pass, 12 fail (total: 71)
  low: 0 pass, 216 fail (total: 216)
  medium: 0 pass, 156 fail (total: 156)
Arriba filter: 443 rows -> 59 PASS; wrote FFPE_HD789_01_RNA_13_B23MVV7LT4_1.arriba.fusions.filtered.tsv and FFPE_HD789_01_RNA_13_B23MVV7LT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: FFPE_HD789_01_RNA_13_B23MVV7LT4_1.arriba.fusions.filter_summary.txt