Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/51/ecd07bea199fb193499e115d0fab21/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/51/ecd07bea199fb193499e115d0fab21/.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/ac/2d574231ca6467ae3edbaf75873ca5/659_cIX-T1-TRNA-1_B23WHTKLT4_1.arriba.fusions.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/stage-6a8e5f46-8592-47ae-b09e-a1efe7f02cb2/6a/80a8f8c27f6b00a3a33e35ea914965/arriba_filter_config.yaml
==> STAGING COMPLETE (5 inputs)

  AIH curated blacklist: matched 4 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 135
  Pass (FILTER=PASS): 15 (11.1%)
  Fail (FILTER=FAIL): 120 (88.9%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 4
  All 4 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(medium<high): 29
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 14
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 13
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0): 10
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 8
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 8
  confidence_below_min(low<high): 7
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 6
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 6
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 3
  total_reads_below_min(3.0<8.0): 3
  confidence_below_min(medium<high);total_reads_below_min(2.0<8.0): 3
  confidence_below_min(low<high);total_reads_below_min(6.0<8.0): 2
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0);aih_curated_blacklist: 2
  aih_curated_blacklist: 1

Breakdown by confidence:
  high: 15 pass, 7 fail (total: 22)
  low: 0 pass, 49 fail (total: 49)
  medium: 0 pass, 64 fail (total: 64)
Arriba filter: 135 rows -> 15 PASS; wrote 659_cIX-T1-TRNA-1_B23WHTKLT4_1.arriba.fusions.filtered.tsv and 659_cIX-T1-TRNA-1_B23WHTKLT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: 659_cIX-T1-TRNA-1_B23WHTKLT4_1.arriba.fusions.filter_summary.txt