Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d3/f5af002abb4c7e886f964e3b6a588c/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d3/f5af002abb4c7e886f964e3b6a588c/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8b/be32785851e3bed2681aa5b2f3e122/tih_rna_sample_00614_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 14 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 334
  Pass (FILTER=PASS): 63 (18.9%)
  Fail (FILTER=FAIL): 271 (81.1%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 14
  All 14 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): 38
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 32
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0): 19
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 16
  confidence_below_min(low<high): 14
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 13
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 10
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 9
  confidence_below_min(medium<high);total_reads_below_min(6.0<8.0): 6
  confidence_below_min(medium<high);total_reads_below_min(7.0<8.0): 6
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 6
  confidence_below_min(medium<high);total_reads_below_min(2.0<8.0): 5
  total_reads_below_min(7.0<8.0): 5
  total_reads_below_min(3.0<8.0): 4

Breakdown by confidence:
  high: 63 pass, 12 fail (total: 75)
  low: 0 pass, 125 fail (total: 125)
  medium: 0 pass, 134 fail (total: 134)
Arriba filter: 334 rows -> 63 PASS; wrote tih_rna_sample_00614_B23MVV7LT4_1.arriba.fusions.filtered.tsv and tih_rna_sample_00614_B23MVV7LT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: tih_rna_sample_00614_B23MVV7LT4_1.arriba.fusions.filter_summary.txt