Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6d/248ad526dba042ca475d030c79246e/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6d/248ad526dba042ca475d030c79246e/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e2/28cc9abba0478bd1ef6495d8eb0cd4/1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2.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 12 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 292
  Pass (FILTER=PASS): 34 (11.6%)
  Fail (FILTER=FAIL): 258 (88.4%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 12
  All 12 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(medium<high): 85
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 33
  confidence_below_min(low<high): 22
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 22
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 16
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 14
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 12
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0): 9
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 7
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 6
  confidence_below_min(medium<high);aih_curated_blacklist: 5
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 5
  confidence_below_min(medium<high);total_reads_below_min(6.0<8.0): 4
  confidence_below_min(low<high);total_reads_below_min(7.0<8.0): 4
  confidence_below_min(medium<high);total_reads_below_min(2.0<8.0): 3

Breakdown by confidence:
  high: 34 pass, 3 fail (total: 37)
  low: 0 pass, 107 fail (total: 107)
  medium: 0 pass, 148 fail (total: 148)
Arriba filter: 292 rows -> 34 PASS; wrote 1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2.arriba.fusions.filtered.tsv and 1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2.arriba.fusions.filtered_pass_only.tsv
Summary written to: 1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2.arriba.fusions.filter_summary.txt