Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6d/75c270b2ae237f7c1c874336c32206/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/43/67da210ae329286e0c5d2fc6ca77af/659_bua-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6d/75c270b2ae237f7c1c874336c32206/.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/stage-40cc52c0-5bec-40b6-b04d-c64c51f55eff/cf/a844d18c3db3aeda7471fb3d005c4f/arriba_filter_config.yaml
==> STAGING COMPLETE (5 inputs)

  AIH curated blacklist: matched 15 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 240
  Pass (FILTER=PASS): 14 (5.8%)
  Fail (FILTER=FAIL): 226 (94.2%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 15
  All 15 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 36
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0): 34
  confidence_below_min(medium<high): 33
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 15
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 15
  confidence_below_min(medium<high);total_reads_below_min(6.0<8.0): 13
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 12
  confidence_below_min(low<high): 12
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 10
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 9
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 6
  confidence_below_min(medium<high);aih_curated_blacklist: 6
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 5
  confidence_below_min(low<high);total_reads_below_min(6.0<8.0): 4
  confidence_below_min(medium<high);total_reads_below_min(2.0<8.0): 3

Breakdown by confidence:
  high: 14 pass, 2 fail (total: 16)
  low: 0 pass, 115 fail (total: 115)
  medium: 0 pass, 109 fail (total: 109)
Arriba filter: 240 rows -> 14 PASS; wrote 659_bua-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.filtered.tsv and 659_bua-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: 659_bua-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.filter_summary.txt