Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/05/da39a129f0f062d491d5b34da57a92/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ba/9ffa69247a281c22e02b7685d5fdd2/KG1_FFPE_01_RNA_0003_B23LG7FLT4_3.arriba.fusions.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/05/da39a129f0f062d491d5b34da57a92/.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-6ef41cd9-2e18-4687-842c-3f6f49c5643f/f2/edcdb43d4676ed2a5254ed1bf31faa/arriba_filter_config.yaml
==> STAGING COMPLETE (5 inputs)

  AIH curated blacklist: matched 5 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 249
  Pass (FILTER=PASS): 30 (12.0%)
  Fail (FILTER=FAIL): 219 (88.0%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 5
  All 5 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 44
  confidence_below_min(medium<high): 28
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 22
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 20
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 19
  confidence_below_min(low<high): 17
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 14
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 12
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 9
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 4
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0): 4
  confidence_below_min(medium<high);total_reads_below_min(2.0<8.0): 4
  confidence_below_min(medium<high);total_reads_below_min(6.0<8.0): 4
  confidence_below_min(medium<high);total_reads_below_min(7.0<8.0): 3
  confidence_below_min(medium<high);aih_curated_blacklist: 3

Breakdown by confidence:
  high: 30 pass, 7 fail (total: 37)
  low: 0 pass, 124 fail (total: 124)
  medium: 0 pass, 88 fail (total: 88)
Arriba filter: 249 rows -> 30 PASS; wrote KG1_FFPE_01_RNA_0003_B23LG7FLT4_3.arriba.fusions.filtered.tsv and KG1_FFPE_01_RNA_0003_B23LG7FLT4_3.arriba.fusions.filtered_pass_only.tsv
Summary written to: KG1_FFPE_01_RNA_0003_B23LG7FLT4_3.arriba.fusions.filter_summary.txt