Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/69/b2e37e5264cfbd328863428632222a/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2d/33971a3a0a0b06dcc9c204f9cb4928/EndoN_FFPE_L01_RNA_01_B23LG7FLT4_1.arriba.fusions.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/69/b2e37e5264cfbd328863428632222a/.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-f79a17a0-988d-46c3-a0fc-cc7f26b06d9c/2f/783d5e3fc4bb0e4fc378bb3e8b5e61/arriba_filter_config.yaml
==> STAGING COMPLETE (5 inputs)

  AIH curated blacklist: matched 4 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 86
  Pass (FILTER=PASS): 0 (0.0%)
  Fail (FILTER=FAIL): 86 (100.0%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 4
  All 4 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(medium<high): 20
  confidence_below_min(medium<high);total_reads_below_min(7.0<8.0): 11
  confidence_below_min(medium<high);total_reads_below_min(6.0<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(3.0<8.0): 9
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 5
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 4
  confidence_below_min(medium<high);aih_curated_blacklist: 3
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 3
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 3
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0): 2
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 2
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 2
  confidence_below_min(low<high): 1
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0);aih_curated_blacklist: 1

Breakdown by confidence:
  low: 0 pass, 28 fail (total: 28)
  medium: 0 pass, 58 fail (total: 58)
Arriba filter: 86 rows -> 0 PASS; wrote EndoN_FFPE_L01_RNA_01_B23LG7FLT4_1.arriba.fusions.filtered.tsv and EndoN_FFPE_L01_RNA_01_B23LG7FLT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: EndoN_FFPE_L01_RNA_01_B23LG7FLT4_1.arriba.fusions.filter_summary.txt