Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8e/2904cfbe29b3bba6f4846ae1311d6e/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8e/2904cfbe29b3bba6f4846ae1311d6e/.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/98/adfc319a45600c8524606bc1fa59b4/V4_0001_RNA_0005_23H5VFLT4_s17.arriba.fusions.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/stage-5b456d70-fab3-4fcc-916c-bc437f411fba/48/d36e0303d259ad82d7d96e756f6134/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: 117
  Pass (FILTER=PASS): 18 (15.4%)
  Fail (FILTER=FAIL): 99 (84.6%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 6
  All 6 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 18
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 12
  confidence_below_min(low<high): 10
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 10
  confidence_below_min(medium<high): 9
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 8
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 7
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 5
  confidence_below_min(low<high);total_reads_below_min(7.0<8.0): 4
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 4
  confidence_below_min(medium<high);aih_curated_blacklist: 3
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 3
  confidence_below_min(low<high);total_reads_below_min(6.0<8.0): 2
  confidence_below_min(medium<high);total_reads_below_min(6.0<8.0): 1
  aih_curated_blacklist: 1

Breakdown by confidence:
  high: 18 pass, 1 fail (total: 19)
  low: 0 pass, 77 fail (total: 77)
  medium: 0 pass, 21 fail (total: 21)
Arriba filter: 117 rows -> 18 PASS; wrote V4_0001_RNA_0005_23H5VFLT4_s17.arriba.fusions.filtered.tsv and V4_0001_RNA_0005_23H5VFLT4_s17.arriba.fusions.filtered_pass_only.tsv
Summary written to: V4_0001_RNA_0005_23H5VFLT4_s17.arriba.fusions.filter_summary.txt