Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/70/8060137b6bcf59b080ac98dae04ef5/659_cfy-T1-TRNA-1_B23WHTKLT4_1.arriba.fusions.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/96/a0f43e325e9866f328851adef8ff12/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/96/a0f43e325e9866f328851adef8ff12/.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-99ebc9bd-f9f1-4b2c-b9a0-02ddaf99f257/ee/adda01b2d23fdd27de06edfd21ea26/arriba_filter_config.yaml
==> STAGING COMPLETE (5 inputs)

  AIH curated blacklist: matched 6 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 160
  Pass (FILTER=PASS): 7 (4.4%)
  Fail (FILTER=FAIL): 153 (95.6%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 6
  All 6 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(medium<high): 42
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0): 22
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 16
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 14
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 11
  confidence_below_min(low<high): 10
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 7
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 5
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 5
  confidence_below_min(medium<high);total_reads_below_min(7.0<8.0): 4
  confidence_below_min(medium<high);total_reads_below_min(6.0<8.0): 3
  confidence_below_min(medium<high);aih_curated_blacklist: 2
  confidence_below_min(low<high);total_reads_below_min(6.0<8.0);aih_curated_blacklist: 2
  confidence_below_min(low<high);total_reads_below_min(6.0<8.0): 2
  aih_curated_blacklist: 1

Breakdown by confidence:
  high: 7 pass, 4 fail (total: 11)
  low: 0 pass, 60 fail (total: 60)
  medium: 0 pass, 89 fail (total: 89)
Arriba filter: 160 rows -> 7 PASS; wrote 659_cfy-T1-TRNA-1_B23WHTKLT4_1.arriba.fusions.filtered.tsv and 659_cfy-T1-TRNA-1_B23WHTKLT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: 659_cfy-T1-TRNA-1_B23WHTKLT4_1.arriba.fusions.filter_summary.txt