Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/81/d054da01825f86512d19ab89d9c13c/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/81/d054da01825f86512d19ab89d9c13c/.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/63/5afbbd9ab2801f5f6824bbeffac822/V4_0001_RNA_0005_23H5VFLT4_s15.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 8 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 91
  Pass (FILTER=PASS): 9 (9.9%)
  Fail (FILTER=FAIL): 82 (90.1%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 8
  All 8 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 13
  confidence_below_min(medium<high): 11
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 10
  confidence_below_min(low<high);total_reads_below_min(0.0<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): 5
  confidence_below_min(low<high);total_reads_below_min(7.0<8.0): 3
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 3
  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(5.0<8.0): 3
  aih_curated_blacklist: 2
  total_reads_below_min(6.0<8.0): 2
  confidence_below_min(low<high): 1
  total_reads_below_min(7.0<8.0): 1

Breakdown by confidence:
  high: 9 pass, 6 fail (total: 15)
  low: 0 pass, 54 fail (total: 54)
  medium: 0 pass, 22 fail (total: 22)
Arriba filter: 91 rows -> 9 PASS; wrote V4_0001_RNA_0005_23H5VFLT4_s15.arriba.fusions.filtered.tsv and V4_0001_RNA_0005_23H5VFLT4_s15.arriba.fusions.filtered_pass_only.tsv
Summary written to: V4_0001_RNA_0005_23H5VFLT4_s15.arriba.fusions.filter_summary.txt