Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b6/cfd775d84395e293de2d0317567d85/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b6/cfd775d84395e293de2d0317567d85/.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/85/4afbc6099bc35c7431d35be3dc891d/659_bGW-T1-TRNA-1_B23WHTKLT4_1.arriba.fusions.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/stage-99ebc9bd-f9f1-4b2c-b9a0-02ddaf99f257/ee/adda01b2d23fdd27de06edfd21ea26/arriba_filter_config.yaml
==> STAGING COMPLETE (5 inputs)

  AIH curated blacklist: matched 9 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 163
  Pass (FILTER=PASS): 13 (8.0%)
  Fail (FILTER=FAIL): 150 (92.0%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 9
  All 9 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(medium<high): 55
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0): 14
  confidence_below_min(low<high);total_reads_below_min(2.0<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(1.0<8.0): 10
  confidence_below_min(medium<high);total_reads_below_min(7.0<8.0): 10
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 6
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 6
  confidence_below_min(medium<high);aih_curated_blacklist: 5
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 4
  confidence_below_min(low<high): 3
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 3
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 3
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0);aih_curated_blacklist: 2
  total_reads_below_min(3.0<8.0);aih_curated_blacklist: 1

Breakdown by confidence:
  high: 13 pass, 1 fail (total: 14)
  low: 0 pass, 46 fail (total: 46)
  medium: 0 pass, 103 fail (total: 103)
Arriba filter: 163 rows -> 13 PASS; wrote 659_bGW-T1-TRNA-1_B23WHTKLT4_1.arriba.fusions.filtered.tsv and 659_bGW-T1-TRNA-1_B23WHTKLT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: 659_bGW-T1-TRNA-1_B23WHTKLT4_1.arriba.fusions.filter_summary.txt