Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/18/f18dfaf7409a54c511a1a69741b2f1/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/18/f18dfaf7409a54c511a1a69741b2f1/.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/ee/b75db425a8b0b0f10259a60dcc4f73/aih-tih-sc-522d83-R1_B23WHYVLT4_1.arriba.fusions.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/stage-8900cb43-4dca-49ac-a290-1d176a2e0012/49/8453bafeca2d0250d89cdefd7ba73e/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: 224
  Pass (FILTER=PASS): 13 (5.8%)
  Fail (FILTER=FAIL): 211 (94.2%)

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

Failure reasons (top 15):
  confidence_below_min(medium<high): 80
  confidence_below_min(low<high): 41
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 16
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 12
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 11
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 8
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 8
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 6
  total_reads_below_min(3.0<8.0): 4
  confidence_below_min(medium<high);total_reads_below_min(6.0<8.0): 4
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 4
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0): 3
  confidence_below_min(medium<high);total_reads_below_min(2.0<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(7.0<8.0): 2

Breakdown by confidence:
  high: 13 pass, 7 fail (total: 20)
  low: 0 pass, 100 fail (total: 100)
  medium: 0 pass, 104 fail (total: 104)
Arriba filter: 224 rows -> 13 PASS; wrote aih-tih-sc-522d83-R1_B23WHYVLT4_1.arriba.fusions.filtered.tsv and aih-tih-sc-522d83-R1_B23WHYVLT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: aih-tih-sc-522d83-R1_B23WHYVLT4_1.arriba.fusions.filter_summary.txt