Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/cc/985eb5caabdee5a66699319b7dd021/tih_rna_sample_00739_B23MVV7LT4_1.arriba.fusions.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a5/7ba4148eb0d590e5dc4d39440587b7/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a5/7ba4148eb0d590e5dc4d39440587b7/.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 14 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 292
  Pass (FILTER=PASS): 5 (1.7%)
  Fail (FILTER=FAIL): 287 (98.3%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 14
  All 14 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(medium<high): 81
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 53
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 31
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 20
  confidence_below_min(low<high): 19
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0): 16
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 16
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 11
  confidence_below_min(medium<high);aih_curated_blacklist: 7
  confidence_below_min(medium<high);total_reads_below_min(2.0<8.0): 6
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 6
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 5
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 3
  confidence_below_min(low<high);total_reads_below_min(6.0<8.0): 3
  aih_curated_blacklist: 2

Breakdown by confidence:
  high: 5 pass, 4 fail (total: 9)
  low: 0 pass, 151 fail (total: 151)
  medium: 0 pass, 132 fail (total: 132)
Arriba filter: 292 rows -> 5 PASS; wrote tih_rna_sample_00739_B23MVV7LT4_1.arriba.fusions.filtered.tsv and tih_rna_sample_00739_B23MVV7LT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: tih_rna_sample_00739_B23MVV7LT4_1.arriba.fusions.filter_summary.txt