Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/26/4f7c7bd64e9559e4d0b3fd518bdb9e/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/26/4f7c7bd64e9559e4d0b3fd518bdb9e/.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/c4/c857ddc4c3b1bc8e2ec77ecf774050/tih_rna_sample_00658_B23MVV7LT4_1.arriba.fusions.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 11 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 233
  Pass (FILTER=PASS): 35 (15.0%)
  Fail (FILTER=FAIL): 198 (85.0%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 11
  All 11 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(medium<high): 64
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 26
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 15
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 15
  confidence_below_min(medium<high);total_reads_below_min(6.0<8.0): 13
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 10
  confidence_below_min(low<high): 9
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0): 8
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 8
  confidence_below_min(medium<high);aih_curated_blacklist: 7
  confidence_below_min(low<high);total_reads_below_min(4.0<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
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 3
  total_reads_below_min(5.0<8.0): 2

Breakdown by confidence:
  high: 35 pass, 4 fail (total: 39)
  low: 0 pass, 87 fail (total: 87)
  medium: 0 pass, 107 fail (total: 107)
Arriba filter: 233 rows -> 35 PASS; wrote tih_rna_sample_00658_B23MVV7LT4_1.arriba.fusions.filtered.tsv and tih_rna_sample_00658_B23MVV7LT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: tih_rna_sample_00658_B23MVV7LT4_1.arriba.fusions.filter_summary.txt