Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/39/4ddf15cd938156f0b383719b3fd795/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/39/4ddf15cd938156f0b383719b3fd795/.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/dd/2814b0c38f453dc1b85396a7ecca1f/tih_rna_sample_00598_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 5 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 75
  Pass (FILTER=PASS): 14 (18.7%)
  Fail (FILTER=FAIL): 61 (81.3%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 5
  All 5 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 12
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 10
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 5
  confidence_below_min(medium<high): 4
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 4
  confidence_below_min(medium<high);total_reads_below_min(2.0<8.0): 3
  confidence_below_min(medium<high);aih_curated_blacklist: 3
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0): 3
  confidence_below_min(low<high): 3
  confidence_below_min(medium<high);total_reads_below_min(7.0<8.0): 2
  total_reads_below_min(7.0<8.0): 2
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 2
  confidence_below_min(low<high);total_reads_below_min(7.0<8.0): 2
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0);aih_curated_blacklist: 2
  total_reads_below_min(6.0<8.0): 1

Breakdown by confidence:
  high: 14 pass, 5 fail (total: 19)
  low: 0 pass, 35 fail (total: 35)
  medium: 0 pass, 21 fail (total: 21)
Arriba filter: 75 rows -> 14 PASS; wrote tih_rna_sample_00598_B23MVV7LT4_1.arriba.fusions.filtered.tsv and tih_rna_sample_00598_B23MVV7LT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: tih_rna_sample_00598_B23MVV7LT4_1.arriba.fusions.filter_summary.txt