Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ba/8eb7be976f8682acf87f81c5c86bb1/659_cVw-T1-TRNA-1_B23WHTKLT4_1.arriba.fusions.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b9/8a3feafa12c376ca689b1bf0ccab8e/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b9/8a3feafa12c376ca689b1bf0ccab8e/.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 10 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 123
  Pass (FILTER=PASS): 6 (4.9%)
  Fail (FILTER=FAIL): 117 (95.1%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 10
  All 10 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 21
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 13
  confidence_below_min(medium<high): 11
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 11
  confidence_below_min(medium<high);total_reads_below_min(7.0<8.0): 10
  confidence_below_min(medium<high);total_reads_below_min(2.0<8.0): 10
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 6
  confidence_below_min(low<high): 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);total_reads_below_min(7.0<8.0): 3
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 3
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 3
  aih_curated_blacklist: 1
  total_reads_below_min(5.0<8.0): 1

Breakdown by confidence:
  high: 6 pass, 4 fail (total: 10)
  low: 0 pass, 60 fail (total: 60)
  medium: 0 pass, 53 fail (total: 53)
Arriba filter: 123 rows -> 6 PASS; wrote 659_cVw-T1-TRNA-1_B23WHTKLT4_1.arriba.fusions.filtered.tsv and 659_cVw-T1-TRNA-1_B23WHTKLT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: 659_cVw-T1-TRNA-1_B23WHTKLT4_1.arriba.fusions.filter_summary.txt