Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c2/b6852abbb3fd82b212a5f2c035fef8/1173_9C_T1_RNA_SLD_01_A23T55JLT4_1.arriba.fusions.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ad/f4149e16eafc2d2cd72ce7c92d0df6/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ad/f4149e16eafc2d2cd72ce7c92d0df6/.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-fe242a7f-c5b9-4d3f-88fa-f3e739280d3a/0e/64006b836d7933c012afba79f66ebb/arriba_filter_config.yaml
==> STAGING COMPLETE (5 inputs)

  AIH curated blacklist: matched 7 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 349
  Pass (FILTER=PASS): 30 (8.6%)
  Fail (FILTER=FAIL): 319 (91.4%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 7
  All 7 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(medium<high): 105
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 48
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 23
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 19
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0): 18
  confidence_below_min(low<high): 17
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 13
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 11
  confidence_below_min(medium<high);total_reads_below_min(6.0<8.0): 11
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 10
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 10
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 9
  confidence_below_min(medium<high);total_reads_below_min(7.0<8.0): 8
  confidence_below_min(medium<high);aih_curated_blacklist: 5
  confidence_below_min(low<high);total_reads_below_min(6.0<8.0): 4

Breakdown by confidence:
  high: 30 pass, 2 fail (total: 32)
  low: 0 pass, 125 fail (total: 125)
  medium: 0 pass, 192 fail (total: 192)
Arriba filter: 349 rows -> 30 PASS; wrote 1173_9C_T1_RNA_SLD_01_A23T55JLT4_1.arriba.fusions.filtered.tsv and 1173_9C_T1_RNA_SLD_01_A23T55JLT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: 1173_9C_T1_RNA_SLD_01_A23T55JLT4_1.arriba.fusions.filter_summary.txt