Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/41/7518fa661e7b31fa6e9d135f7016e7/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/41/7518fa661e7b31fa6e9d135f7016e7/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/12/f75080bef6a98bc8e15152fdb3251d/1173_M5U_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 11 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 275
  Pass (FILTER=PASS): 24 (8.7%)
  Fail (FILTER=FAIL): 251 (91.3%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 11
  All 11 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(medium<high): 68
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 27
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 26
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 19
  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): 16
  confidence_below_min(medium<high);total_reads_below_min(6.0<8.0): 14
  confidence_below_min(low<high): 12
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 11
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 10
  confidence_below_min(medium<high);aih_curated_blacklist: 5
  confidence_below_min(medium<high);total_reads_below_min(7.0<8.0): 4
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 4
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 3
  confidence_below_min(low<high);total_reads_below_min(7.0<8.0);aih_curated_blacklist: 2

Breakdown by confidence:
  high: 24 pass, 4 fail (total: 28)
  low: 0 pass, 94 fail (total: 94)
  medium: 0 pass, 153 fail (total: 153)
Arriba filter: 275 rows -> 24 PASS; wrote 1173_M5U_T1_RNA_SLD_01_A23T55JLT4_1.arriba.fusions.filtered.tsv and 1173_M5U_T1_RNA_SLD_01_A23T55JLT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: 1173_M5U_T1_RNA_SLD_01_A23T55JLT4_1.arriba.fusions.filter_summary.txt