Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2d/43e7e688e02c7b04fcff74b8c4f0d7/tih_rna_sample_00766_B23MVV7LT4_1.arriba.fusions.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/49/e94d2908a2d811e75e03c1db161478/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/49/e94d2908a2d811e75e03c1db161478/.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-7324c8a8-f474-426a-a5c9-715912777f94/d8/92d6652b0b8fcc763d0f3fff270437/arriba_filter_config.yaml
==> STAGING COMPLETE (5 inputs)

  AIH curated blacklist: matched 8 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 103
  Pass (FILTER=PASS): 12 (11.7%)
  Fail (FILTER=FAIL): 91 (88.3%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 8
  All 8 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 15
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 12
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 12
  confidence_below_min(low<high): 12
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 9
  confidence_below_min(medium<high): 6
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 3
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 2
  confidence_below_min(medium<high);aih_curated_blacklist: 2
  confidence_below_min(low<high);aih_curated_blacklist: 2
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 2
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 2
  total_reads_below_min(7.0<8.0);aih_curated_blacklist: 1
  total_reads_below_min(6.0<8.0): 1
  total_reads_below_min(4.0<8.0): 1

Breakdown by confidence:
  high: 12 pass, 4 fail (total: 16)
  low: 0 pass, 59 fail (total: 59)
  medium: 0 pass, 28 fail (total: 28)
Arriba filter: 103 rows -> 12 PASS; wrote tih_rna_sample_00766_B23MVV7LT4_1.arriba.fusions.filtered.tsv and tih_rna_sample_00766_B23MVV7LT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: tih_rna_sample_00766_B23MVV7LT4_1.arriba.fusions.filter_summary.txt