Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b2/7145d83928e40c7bbe84bad747342c/A673_FFPE_RNA_0001_B23LG7FLT4_3.arriba.fusions.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/04/1e4b5aba306ecc6c809e608f44cd67/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/04/1e4b5aba306ecc6c809e608f44cd67/.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 8 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 261
  Pass (FILTER=PASS): 45 (17.2%)
  Fail (FILTER=FAIL): 216 (82.8%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 8
  All 8 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): 27
  confidence_below_min(medium<high);total_reads_below_min(6.0<8.0): 25
  confidence_below_min(low<high): 17
  confidence_below_min(low<high);total_reads_below_min(4.0<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): 12
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 11
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 9
  confidence_below_min(low<high);total_reads_below_min(6.0<8.0): 8
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 7
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 5
  confidence_below_min(medium<high);aih_curated_blacklist: 4
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0): 3
  confidence_below_min(medium<high);total_reads_below_min(7.0<8.0): 2

Breakdown by confidence:
  high: 45 pass, 2 fail (total: 47)
  low: 0 pass, 112 fail (total: 112)
  medium: 0 pass, 102 fail (total: 102)
Arriba filter: 261 rows -> 45 PASS; wrote A673_FFPE_RNA_0001_B23LG7FLT4_3.arriba.fusions.filtered.tsv and A673_FFPE_RNA_0001_B23LG7FLT4_3.arriba.fusions.filtered_pass_only.tsv
Summary written to: A673_FFPE_RNA_0001_B23LG7FLT4_3.arriba.fusions.filter_summary.txt