Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/04/0965feab12df90bc291e7626e33cc2/aih-tih-sc-8353c5-R1_A23WJ53LT4_1.arriba.fusions.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/cd/4978b24459fbb8e4f108846f0e4f2a/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/cd/4978b24459fbb8e4f108846f0e4f2a/.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-5ae5f7b1-ce8a-4a12-9374-820c751df9c5/09/a7ecdb27117590dd6e7bf9e221420e/arriba_filter_config.yaml
==> STAGING COMPLETE (5 inputs)

  AIH curated blacklist: matched 13 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 311
  Pass (FILTER=PASS): 46 (14.8%)
  Fail (FILTER=FAIL): 265 (85.2%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 13
  All 13 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 45
  confidence_below_min(medium<high): 39
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 31
  confidence_below_min(low<high): 25
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 21
  confidence_below_min(medium<high);total_reads_below_min(6.0<8.0): 17
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 17
  confidence_below_min(medium<high);total_reads_below_min(7.0<8.0): 14
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 8
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 8
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 5
  confidence_below_min(medium<high);aih_curated_blacklist: 5
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 5
  confidence_below_min(medium<high);total_reads_below_min(2.0<8.0): 4
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0): 4

Breakdown by confidence:
  high: 46 pass, 5 fail (total: 51)
  low: 0 pass, 136 fail (total: 136)
  medium: 0 pass, 124 fail (total: 124)
Arriba filter: 311 rows -> 46 PASS; wrote aih-tih-sc-8353c5-R1_A23WJ53LT4_1.arriba.fusions.filtered.tsv and aih-tih-sc-8353c5-R1_A23WJ53LT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: aih-tih-sc-8353c5-R1_A23WJ53LT4_1.arriba.fusions.filter_summary.txt