Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/95/e7bfc8e55997a024640548549fc1d0/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/95/e7bfc8e55997a024640548549fc1d0/.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/b7/6b8d299367ac29fef0ed37ca30d843/aih-tih-sc-445ab1-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 8 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 363
  Pass (FILTER=PASS): 51 (14.0%)
  Fail (FILTER=FAIL): 312 (86.0%)

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

Failure reasons (top 15):
  confidence_below_min(medium<high): 74
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 39
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 29
  confidence_below_min(low<high): 23
  confidence_below_min(medium<high);total_reads_below_min(7.0<8.0): 23
  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(0.0<8.0): 13
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 12
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0): 11
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 10
  confidence_below_min(medium<high);total_reads_below_min(2.0<8.0): 9
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 9
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 8
  total_reads_below_min(5.0<8.0): 6

Breakdown by confidence:
  high: 51 pass, 10 fail (total: 61)
  low: 0 pass, 125 fail (total: 125)
  medium: 0 pass, 177 fail (total: 177)
Arriba filter: 363 rows -> 51 PASS; wrote aih-tih-sc-445ab1-R1_B23WHYVLT4_1.arriba.fusions.filtered.tsv and aih-tih-sc-445ab1-R1_B23WHYVLT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: aih-tih-sc-445ab1-R1_B23WHYVLT4_1.arriba.fusions.filter_summary.txt