Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/46/1f14c8881a5cd432066a706e1660e8/tih_rna_sample_00127_23H5VFLT4_s08.arriba.fusions.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a0/ef6d53eb35849b8f500965c4f6c679/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a0/ef6d53eb35849b8f500965c4f6c679/.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/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: 169
  Pass (FILTER=PASS): 5 (3.0%)
  Fail (FILTER=FAIL): 164 (97.0%)

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

Failure reasons (top 15):
  confidence_below_min(medium<high): 72
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 11
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 10
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 10
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 9
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 9
  confidence_below_min(medium<high);total_reads_below_min(7.0<8.0): 6
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0): 5
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 4
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0);aih_curated_blacklist: 4
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 4
  confidence_below_min(low<high): 3
  confidence_below_min(medium<high);aih_curated_blacklist: 3
  confidence_below_min(medium<high);total_reads_below_min(2.0<8.0): 2
  total_reads_below_min(7.0<8.0): 2

Breakdown by confidence:
  high: 5 pass, 6 fail (total: 11)
  low: 0 pass, 50 fail (total: 50)
  medium: 0 pass, 108 fail (total: 108)
Arriba filter: 169 rows -> 5 PASS; wrote tih_rna_sample_00127_23H5VFLT4_s08.arriba.fusions.filtered.tsv and tih_rna_sample_00127_23H5VFLT4_s08.arriba.fusions.filtered_pass_only.tsv
Summary written to: tih_rna_sample_00127_23H5VFLT4_s08.arriba.fusions.filter_summary.txt