Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1e/f29914ccc0b027806991425c50665e/FFPE_HD789_02_RNA_0015_B23MHV2LT4_1.arriba.fusions.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/cd/b42349171fccc1190f88041d5e45b4/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/cd/b42349171fccc1190f88041d5e45b4/.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-40cc52c0-5bec-40b6-b04d-c64c51f55eff/cf/a844d18c3db3aeda7471fb3d005c4f/arriba_filter_config.yaml
==> STAGING COMPLETE (5 inputs)

  AIH curated blacklist: matched 15 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 491
  Pass (FILTER=PASS): 77 (15.7%)
  Fail (FILTER=FAIL): 414 (84.3%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 15
  All 15 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(medium<high): 112
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 86
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 32
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 23
  confidence_below_min(low<high): 23
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 20
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 20
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 17
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 13
  confidence_below_min(medium<high);total_reads_below_min(7.0<8.0): 10
  confidence_below_min(medium<high);total_reads_below_min(2.0<8.0): 8
  confidence_below_min(low<high);total_reads_below_min(6.0<8.0): 7
  confidence_below_min(medium<high);total_reads_below_min(6.0<8.0): 6
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 6
  confidence_below_min(medium<high);aih_curated_blacklist: 6

Breakdown by confidence:
  high: 77 pass, 11 fail (total: 88)
  low: 0 pass, 202 fail (total: 202)
  medium: 0 pass, 201 fail (total: 201)
Arriba filter: 491 rows -> 77 PASS; wrote FFPE_HD789_02_RNA_0015_B23MHV2LT4_1.arriba.fusions.filtered.tsv and FFPE_HD789_02_RNA_0015_B23MHV2LT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: FFPE_HD789_02_RNA_0015_B23MHV2LT4_1.arriba.fusions.filter_summary.txt