Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c7/27e74b8863b356de643b497da74095/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b7/d66ea226d531df5f19fc4021a1f89d/tih_rna_sample_00692_B23MVV7LT4_1.arriba.fusions.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c7/27e74b8863b356de643b497da74095/.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 4 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 76
  Pass (FILTER=PASS): 4 (5.3%)
  Fail (FILTER=FAIL): 72 (94.7%)

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

Failure reasons (top 15):
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 14
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 11
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 8
  confidence_below_min(medium<high): 7
  confidence_below_min(low<high): 7
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 6
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 3
  total_reads_below_min(4.0<8.0): 2
  confidence_below_min(medium<high);aih_curated_blacklist: 2
  confidence_below_min(medium<high);total_reads_below_min(2.0<8.0): 2
  confidence_below_min(low<high);total_reads_below_min(6.0<8.0): 2
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 2
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 2
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0): 1
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 1

Breakdown by confidence:
  high: 4 pass, 2 fail (total: 6)
  low: 0 pass, 54 fail (total: 54)
  medium: 0 pass, 16 fail (total: 16)
Arriba filter: 76 rows -> 4 PASS; wrote tih_rna_sample_00692_B23MVV7LT4_1.arriba.fusions.filtered.tsv and tih_rna_sample_00692_B23MVV7LT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: tih_rna_sample_00692_B23MVV7LT4_1.arriba.fusions.filter_summary.txt