Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4d/c789cbef191c750f4a5eb8b76bbc56/tih_rna_sample_00669_B23MVV7LT4_1.arriba.fusions.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/24/9d9e142cb7b8c5b8d4fc7125c32768/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/24/9d9e142cb7b8c5b8d4fc7125c32768/.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 7 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 217
  Pass (FILTER=PASS): 12 (5.5%)
  Fail (FILTER=FAIL): 205 (94.5%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 7
  All 7 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(medium<high): 54
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0): 23
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 19
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 19
  confidence_below_min(low<high): 15
  confidence_below_min(medium<high);total_reads_below_min(6.0<8.0): 14
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 13
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 11
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 7
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 6
  confidence_below_min(low<high);total_reads_below_min(7.0<8.0): 4
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 4
  confidence_below_min(low<high);total_reads_below_min(6.0<8.0): 3
  confidence_below_min(medium<high);aih_curated_blacklist: 3
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 3

Breakdown by confidence:
  high: 12 pass, 2 fail (total: 14)
  low: 0 pass, 90 fail (total: 90)
  medium: 0 pass, 113 fail (total: 113)
Arriba filter: 217 rows -> 12 PASS; wrote tih_rna_sample_00669_B23MVV7LT4_1.arriba.fusions.filtered.tsv and tih_rna_sample_00669_B23MVV7LT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: tih_rna_sample_00669_B23MVV7LT4_1.arriba.fusions.filter_summary.txt