Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c9/c89bc97cb6d7abe1f863153932beba/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c9/c89bc97cb6d7abe1f863153932beba/.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/5c/3481ec030ead2f0c2d77b833061166/aih-tih-sc-ce6733-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 10 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 303
  Pass (FILTER=PASS): 28 (9.2%)
  Fail (FILTER=FAIL): 275 (90.8%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 10
  All 10 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(medium<high): 45
  confidence_below_min(medium<high);total_reads_below_min(6.0<8.0): 33
  confidence_below_min(low<high): 32
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 25
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 23
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 20
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 17
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 12
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 12
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 9
  confidence_below_min(medium<high);total_reads_below_min(2.0<8.0): 9
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0): 8
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 5
  total_reads_below_min(5.0<8.0): 4
  confidence_below_min(medium<high);total_reads_below_min(7.0<8.0): 4

Breakdown by confidence:
  high: 28 pass, 10 fail (total: 38)
  low: 0 pass, 124 fail (total: 124)
  medium: 0 pass, 141 fail (total: 141)
Arriba filter: 303 rows -> 28 PASS; wrote aih-tih-sc-ce6733-R1_B23WHYVLT4_1.arriba.fusions.filtered.tsv and aih-tih-sc-ce6733-R1_B23WHYVLT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: aih-tih-sc-ce6733-R1_B23WHYVLT4_1.arriba.fusions.filter_summary.txt