Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e2/98d2dfbfef8efaf6584506ec4be16d/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e2/98d2dfbfef8efaf6584506ec4be16d/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/88/8d59c169f68dd6a27c6479d45b62c9/tih_rna_sample_00740_B23MVV7LT4_1.arriba.fusions.tsv
  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 8 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 181
  Pass (FILTER=PASS): 6 (3.3%)
  Fail (FILTER=FAIL): 175 (96.7%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 8
  All 8 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 27
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 26
  confidence_below_min(medium<high): 22
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 15
  confidence_below_min(medium<high);total_reads_below_min(6.0<8.0): 12
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 11
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 10
  confidence_below_min(low<high): 10
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 9
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 7
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 4
  confidence_below_min(low<high);total_reads_below_min(7.0<8.0): 4
  confidence_below_min(medium<high);aih_curated_blacklist: 3
  confidence_below_min(low<high);total_reads_below_min(6.0<8.0): 3
  confidence_below_min(medium<high);total_reads_below_min(7.0<8.0): 2

Breakdown by confidence:
  high: 6 pass, 3 fail (total: 9)
  low: 0 pass, 93 fail (total: 93)
  medium: 0 pass, 79 fail (total: 79)
Arriba filter: 181 rows -> 6 PASS; wrote tih_rna_sample_00740_B23MVV7LT4_1.arriba.fusions.filtered.tsv and tih_rna_sample_00740_B23MVV7LT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: tih_rna_sample_00740_B23MVV7LT4_1.arriba.fusions.filter_summary.txt