Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/25/5aa5da4add28962d7cf1d741d9cc03/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/25/5aa5da4add28962d7cf1d741d9cc03/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1c/ca9ffab7011bd4f8ee50c048860f8f/tih_rna_sample_00104_23H5VFLT4_s20.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-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: 46
  Pass (FILTER=PASS): 4 (8.7%)
  Fail (FILTER=FAIL): 42 (91.3%)

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(4.0<8.0): 13
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 12
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 5
  confidence_below_min(medium<high);aih_curated_blacklist: 3
  confidence_below_min(medium<high): 2
  confidence_below_min(medium<high);total_reads_below_min(2.0<8.0): 1
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 1
  confidence_below_min(medium<high);total_reads_below_min(7.0<8.0): 1
  confidence_below_min(low<high): 1
  confidence_below_min(low<high);aih_curated_blacklist: 1
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 1
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0);aih_curated_blacklist: 1

Breakdown by confidence:
  high: 4 pass, 0 fail (total: 4)
  low: 0 pass, 35 fail (total: 35)
  medium: 0 pass, 7 fail (total: 7)
Arriba filter: 46 rows -> 4 PASS; wrote tih_rna_sample_00104_23H5VFLT4_s20.arriba.fusions.filtered.tsv and tih_rna_sample_00104_23H5VFLT4_s20.arriba.fusions.filtered_pass_only.tsv
Summary written to: tih_rna_sample_00104_23H5VFLT4_s20.arriba.fusions.filter_summary.txt