Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7c/a61c1046aa969e386d826c15c7d853/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7c/a61c1046aa969e386d826c15c7d853/.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/33/2c610a9bdb28fd4d575cfef3f17dca/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_1.arriba.fusions.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 6 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 379
  Pass (FILTER=PASS): 74 (19.5%)
  Fail (FILTER=FAIL): 305 (80.5%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 6
  All 6 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): 45
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 26
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 19
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 18
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 16
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 12
  confidence_below_min(low<high): 12
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0): 10
  confidence_below_min(medium<high);total_reads_below_min(6.0<8.0): 7
  confidence_below_min(medium<high);total_reads_below_min(2.0<8.0): 6
  confidence_below_min(low<high);total_reads_below_min(6.0<8.0): 5
  confidence_below_min(medium<high);total_reads_below_min(7.0<8.0): 5
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 5
  confidence_below_min(medium<high);aih_curated_blacklist: 3

Breakdown by confidence:
  high: 74 pass, 6 fail (total: 80)
  low: 0 pass, 134 fail (total: 134)
  medium: 0 pass, 165 fail (total: 165)
Arriba filter: 379 rows -> 74 PASS; wrote 1173_NWE_T1_RNA_SLD_01_A23T55JLT4_1.arriba.fusions.filtered.tsv and 1173_NWE_T1_RNA_SLD_01_A23T55JLT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: 1173_NWE_T1_RNA_SLD_01_A23T55JLT4_1.arriba.fusions.filter_summary.txt