Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ee/1f424179c5eb3902587f347b727d4d/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ee/1f424179c5eb3902587f347b727d4d/.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/34/0a117a320b3652647a05e19e65c201/tih_rna_sample_00762_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: 295
  Pass (FILTER=PASS): 22 (7.5%)
  Fail (FILTER=FAIL): 273 (92.5%)

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

Failure reasons (top 15):
  confidence_below_min(medium<high): 58
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 47
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 31
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 18
  confidence_below_min(low<high): 17
  confidence_below_min(medium<high);total_reads_below_min(6.0<8.0): 16
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 16
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 13
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 11
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 11
  confidence_below_min(medium<high);aih_curated_blacklist: 5
  total_reads_below_min(3.0<8.0): 4
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 4
  confidence_below_min(low<high);total_reads_below_min(7.0<8.0): 4
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0): 2

Breakdown by confidence:
  high: 22 pass, 10 fail (total: 32)
  low: 0 pass, 129 fail (total: 129)
  medium: 0 pass, 134 fail (total: 134)
Arriba filter: 295 rows -> 22 PASS; wrote tih_rna_sample_00762_B23MVV7LT4_1.arriba.fusions.filtered.tsv and tih_rna_sample_00762_B23MVV7LT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: tih_rna_sample_00762_B23MVV7LT4_1.arriba.fusions.filter_summary.txt