Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/03/d5f16edfb18ecc9834d72f097bad80/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/03/d5f16edfb18ecc9834d72f097bad80/.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/7c/fd8267018b43eb9701267511580bf8/659_epP-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 21 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 228
  Pass (FILTER=PASS): 14 (6.1%)
  Fail (FILTER=FAIL): 214 (93.9%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 21
  All 21 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 30
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 29
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 26
  confidence_below_min(medium<high): 25
  confidence_below_min(medium<high);total_reads_below_min(6.0<8.0): 20
  confidence_below_min(medium<high);total_reads_below_min(2.0<8.0): 10
  confidence_below_min(low<high): 9
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 8
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 8
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 7
  confidence_below_min(medium<high);aih_curated_blacklist: 7
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 6
  confidence_below_min(low<high);total_reads_below_min(6.0<8.0): 4
  aih_curated_blacklist: 4
  confidence_below_min(low<high);total_reads_below_min(7.0<8.0): 4

Breakdown by confidence:
  high: 14 pass, 6 fail (total: 20)
  low: 0 pass, 124 fail (total: 124)
  medium: 0 pass, 84 fail (total: 84)
Arriba filter: 228 rows -> 14 PASS; wrote 659_epP-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.filtered.tsv and 659_epP-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: 659_epP-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.filter_summary.txt