Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3e/3d70bf5aba4dcc4ae1fd7dae39a5da/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3e/3d70bf5aba4dcc4ae1fd7dae39a5da/.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/ec/b7a506320ad7a81d377f21fd2157c5/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.arriba.fusions.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/stage-f79a17a0-988d-46c3-a0fc-cc7f26b06d9c/2f/783d5e3fc4bb0e4fc378bb3e8b5e61/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: 340
  Pass (FILTER=PASS): 55 (16.2%)
  Fail (FILTER=FAIL): 285 (83.8%)

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

Failure reasons (top 15):
  confidence_below_min(medium<high): 47
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 44
  confidence_below_min(low<high): 21
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 19
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 18
  confidence_below_min(medium<high);total_reads_below_min(6.0<8.0): 17
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 16
  confidence_below_min(medium<high);total_reads_below_min(7.0<8.0): 15
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 14
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 13
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 12
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0): 9
  confidence_below_min(medium<high);total_reads_below_min(2.0<8.0): 9
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 9
  confidence_below_min(medium<high);aih_curated_blacklist: 3

Breakdown by confidence:
  high: 55 pass, 6 fail (total: 61)
  low: 0 pass, 143 fail (total: 143)
  medium: 0 pass, 136 fail (total: 136)
Arriba filter: 340 rows -> 55 PASS; wrote FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.arriba.fusions.filtered.tsv and FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.arriba.fusions.filter_summary.txt