Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/04/e9ebbf15a3c6ec5adabe5b3fc1b488/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/04/e9ebbf15a3c6ec5adabe5b3fc1b488/.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/80/10f2c459437e9132aad81a69f375a5/GM24385_0001_RNA_0001_23H5VFLT4_s24.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 5 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 48
  Pass (FILTER=PASS): 2 (4.2%)
  Fail (FILTER=FAIL): 46 (95.8%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 5
  All 5 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 8
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 7
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 6
  confidence_below_min(medium<high): 4
  confidence_below_min(low<high): 4
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 4
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 4
  confidence_below_min(medium<high);aih_curated_blacklist: 3
  aih_curated_blacklist: 1
  total_reads_below_min(4.0<8.0): 1
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 1
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0);aih_curated_blacklist: 1
  confidence_below_min(low<high);total_reads_below_min(6.0<8.0): 1
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 1

Breakdown by confidence:
  high: 2 pass, 2 fail (total: 4)
  low: 0 pass, 35 fail (total: 35)
  medium: 0 pass, 9 fail (total: 9)
Arriba filter: 48 rows -> 2 PASS; wrote GM24385_0001_RNA_0001_23H5VFLT4_s24.arriba.fusions.filtered.tsv and GM24385_0001_RNA_0001_23H5VFLT4_s24.arriba.fusions.filtered_pass_only.tsv
Summary written to: GM24385_0001_RNA_0001_23H5VFLT4_s24.arriba.fusions.filter_summary.txt