Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ce/ffef226e0a11b0f6ecc0257a83fbc1/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ce/ffef226e0a11b0f6ecc0257a83fbc1/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b9/c81b531ae14a16274ddb4e4a77788d/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.arriba.fusions.tsv
  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 9 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 223
  Pass (FILTER=PASS): 47 (21.1%)
  Fail (FILTER=FAIL): 176 (78.9%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 9
  All 9 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(medium<high): 47
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 28
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 17
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 13
  confidence_below_min(medium<high);total_reads_below_min(6.0<8.0): 13
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 10
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 7
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 7
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 6
  confidence_below_min(medium<high);aih_curated_blacklist: 4
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0): 4
  confidence_below_min(low<high): 3
  total_reads_below_min(3.0<8.0): 3
  confidence_below_min(medium<high);total_reads_below_min(2.0<8.0): 3
  confidence_below_min(low<high);total_reads_below_min(6.0<8.0): 3

Breakdown by confidence:
  high: 47 pass, 3 fail (total: 50)
  low: 0 pass, 76 fail (total: 76)
  medium: 0 pass, 97 fail (total: 97)
Arriba filter: 223 rows -> 47 PASS; wrote 1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.arriba.fusions.filtered.tsv and 1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: 1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.arriba.fusions.filter_summary.txt