Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/83/86a50d386ebf575a78391d9dc7c5cc/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/83/86a50d386ebf575a78391d9dc7c5cc/.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/89/1e37eb8c2244916ee8db35fe2d90b3/659_bIB-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/stage-40cc52c0-5bec-40b6-b04d-c64c51f55eff/cf/a844d18c3db3aeda7471fb3d005c4f/arriba_filter_config.yaml
==> STAGING COMPLETE (5 inputs)

  AIH curated blacklist: matched 16 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 353
  Pass (FILTER=PASS): 26 (7.4%)
  Fail (FILTER=FAIL): 327 (92.6%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 16
  All 16 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(medium<high): 102
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 77
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 15
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 15
  confidence_below_min(medium<high);total_reads_below_min(6.0<8.0): 14
  confidence_below_min(low<high): 14
  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): 11
  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(2.0<8.0): 8
  confidence_below_min(medium<high);aih_curated_blacklist: 7
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 7
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 5
  confidence_below_min(low<high);total_reads_below_min(6.0<8.0): 5

Breakdown by confidence:
  high: 26 pass, 5 fail (total: 31)
  low: 0 pass, 146 fail (total: 146)
  medium: 0 pass, 176 fail (total: 176)
Arriba filter: 353 rows -> 26 PASS; wrote 659_bIB-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.filtered.tsv and 659_bIB-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: 659_bIB-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.filter_summary.txt