Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/10/92c5430ea7f27a06a78fa48ea69506/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f0/582b522339a13eae43b8de59374a07/tih_rna_sample_00149_B23WHTKLT4_1.arriba.fusions.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/10/92c5430ea7f27a06a78fa48ea69506/.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-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: 133
  Pass (FILTER=PASS): 20 (15.0%)
  Fail (FILTER=FAIL): 113 (85.0%)

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

Failure reasons (top 15):
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 23
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 21
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0): 21
  confidence_below_min(low<high): 8
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 7
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 5
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 5
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 4
  confidence_below_min(medium<high);aih_curated_blacklist: 4
  total_reads_below_min(3.0<8.0): 3
  confidence_below_min(medium<high): 3
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 3
  confidence_below_min(medium<high);total_reads_below_min(2.0<8.0): 2
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 1
  total_reads_below_min(6.0<8.0): 1

Breakdown by confidence:
  high: 20 pass, 5 fail (total: 25)
  low: 0 pass, 47 fail (total: 47)
  medium: 0 pass, 61 fail (total: 61)
Arriba filter: 133 rows -> 20 PASS; wrote tih_rna_sample_00149_B23WHTKLT4_1.arriba.fusions.filtered.tsv and tih_rna_sample_00149_B23WHTKLT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: tih_rna_sample_00149_B23WHTKLT4_1.arriba.fusions.filter_summary.txt